Windows Update Broken After Cloning Hard drive

You just migrated your system to a new hard drive by cloning or restoring a backup.  Things seem to be working, but Windows Update fails.  The error popup says that the service isn’t running but task manager says that it is.  You’ve just been bitten by the new Advanced Format (4k-byte sector) hard drives.

I recently upgraded my ThinkPad T400 (Windows 7 Pro 64) from a 320GB 7200RPM drive to a 500GB 7200RPM drive.  It was a simple process using Acronis: Cloning Hard Drives With Acronis.  I specifically shopped for an older style drive that used 512-byte sectors.

The industry is rapidly going to “Advanced Format” drives that have 4k-type sectors: Advanced Format (wikipedia).  The AF drives can cause problems with performance if their partitions aren’t correctly aligned, especially when running Windows XP.  Unfortunately, the on-line drive documentation I consulted when selecting a drive was incorrect, and I ended up with an AF drive.  I’m running W7 – which supposedly supports AF drives.  It wasn’t that simple…

First, a note about how I ended up with an AF drive.  I was aware of possible issues with 4k-byte sectors, so I specifically looked for a non-AF drive.  My first choice was a Western Digital WD5000BEKT from Amazon.  It worked OK, but was too noisy: Strange Laptop Drive Noise: “Whoosh” Next choice was a Hitachi 0S02858.  All the comments on Amazon indicate that it’s a 7K500-500 drive with 512-byte sectors.  The one I received was actually a 7K750-500 Advanced Format drive.  So was its replacement.  A Hitachi tech told me that the 0S02858 part number indicated a 7K500 drive, and that I should have Amazon replace it.  He later said that Hitachi might ship either model under that part number.  Grrrr!

Back to the Windows Update problem.  Windows 7 is supposed to understand AF drives, and correctly aligns partitions.  Sort of.  Without the updates in a hotfix (or SP1 ??) , Windows can’t detect the drive’s physical sector size, and Update (and some other features) fail.  I was already running SP1, so it should have been OK.  Microsoft explanation and hotfix link: An update that improves the compatibility of Windows 7 and Windows Server 2008 R2 with Advanced Format Disks is available  On my ThinkPad T400, the hotfix just errored out with no additional information.

To cut to the chase, SP1 and the hotfix weren’t correctly updating the storage driver, so it couldn’t report sector size to Windows.  The clue here was that fsutil (see that Microsoft link, above) was reporting “bytes per physical sector” as “<Not Supported>”.

My fix was to manually install the latest Intel driver: Intel® Rapid Storage Technology  (link may be stale – see update below) That installs a lot more than necessary – AFAICS – but was an easy fix.  fsutil now reports the 4096-byte sector size, and Windows Update works.  I’ve also heard that installing the AHCI driver from the Lenovo driver matrix for one of the Huron River ThinkPads (T420/T520/X220/etc) would also do the job w/a smaller install (and less Intel crapware) but I have not tested that.   After updating the storage driver the hotfix happily announced that it (the hotfix) was already installed.

Update 2012.12.12 The Intel driver download is a moving target.  Try this search link if the one above doesn’t work: http://downloadcenter.intel.com/SearchResult.aspx?lang=eng&ProductFamily=Software+Products&ProductLine=Chipset+Software&ProductProduct=Intel%C2%AE+Rapid+Storage+Technology+%28Intel%C2%AE+RST%29

Update 2011.10.04 Have a look at the readme that comes with the Intel driver.  There are some command line options that allow installing the driver only without all the other unnecessary stuff.

Update 2012.10.15 That Intel link target keeps changing.  Try going to Intel.com and searching on “rapid storage technology”.  Pick the latest result that matches your operating system.  Then download the iata_enu.exe and readme files.

For XP users, the story is more painful.  Here are a couple of links to drive manufacturer’s tools – that should help:

Western Digital documentation and tools: Advanced Format Software

Hitachi whitepaper:  Advanced Format Drives   Hitachi Alignment tool:  Hitachi Align tool

Those alignment tools are the private-labeled Acronis alignment tool.

Sorry about the long post.  Hope it helps someone.

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40 Responses to Windows Update Broken After Cloning Hard drive

  1. ziggyboy says:

    Downloading the SP1 update ISO image, burning to a DVD and updating from the burned DVD disk fixed the problem.

    Your method did not work for me for some reason. I’ve got a T410 purchased May/June 2010 that I’ve upgraded to a Seagate Momentus 7200RPM 750GB AF. I then restored Win 7 HP 64-bit using the Lenovo restore DVD’s (factory install) which was not SP1.

    I successfully installed the latest Intel RST driver and it gets detected as a 4K physical drive but Windows Update still didn’t work. Also tried updating to SP1 using the standalone installer but still nothing.

    Then, as last desperate attempt I burned the 2GB SP1 update ISO image from the Microsoft website and voile it just worked! Windows Update immediately worked afterwards!

  2. ArtFD says:

    Your initial post is one of the few I was able to find dealing with AF HDD’s. I now have a combination of your problem & ziggyboy’s problem. Trying to install a Seagate Momentus Model ST9750420AS 750 GB HDD in my Lenovo R500, which had a Seagate 500 GB HDD,upgraded from the OEM 160GB. I used Seagate Disc Wizard to copy the 160GB contents to the 500GB HDD. I had some problem getting the 500GB to boot properly, something to do with hidden/active status of the OEM SYSTEM_DRV partition. The 500 GB HDD has been running fine for months, but it’s been filling up, hence my wish to upgrade to 750 GB. I have 2 identical ST9750420AS drives. I have tried copying/cloning all my partitions from the 500 GB HDD to the 750 GB HDD using Seagate Disc Wizard. The cloned disk is recognized & boots part way into Win 7, then shows an error msg along the lines of “Can’t find AUTOCHK” then a BSOD with a fatal error message. Identical results when I attempted to clone with Macrium Reflect Free 5.0.4033. I have tried cloning with the 750 GB HDD in position it would be running in, or in an external HDD, always the same error message. However, Win 7 did boot partly. I was able to go to the Lenovo recovery partition, which identified a problem but could not fix it. So I ran the recovery routine, to create an OEM status on one of my new 750 GB HDD’s. This started up just fine, no error messages. However, when I went to Windows Update – error msg “Service not running” I had previously secured the SP1 DVD from Microsoft. The DVD had run fine a few months ago to update the Win7 on my 500 GB setup, but it would not run on my new 750 GB setup from the ‘setup.exe’ on the DVD. I copied the 930 MB windows6.1-KB9769432-X64.exe file from the DVD to my 750 GB HDD. When I ran the EXE file locally,I got the expected menu asking for permission to update to SP1, then the first file,followed by an error message saying ‘catastrophic failure’. More on next comment.

  3. ArtFD says:

    I started to wonder if I needed “Intel Rapid Storage Technology.” I downloaded & installed the 6 MB English language version,it installed fine. After rebooting I ran FSUTIL from the CMD window,and got a normal bytes/sector report. However, Windows Update still would not work, same error msg. So I again tried to run the 930 MB SP1 EXE file from my HDD. This time it ran normally, and has been chugging along for 30 minutes. I’ll report later how that works out. There is yet another twist to my story. Remember I bought 2 identical 750 GB HDDs. I downloaded the ISO file to install Win 7 Pro 64 bit from Microsoft, months ago,in the thought that I could install the Microsoft version if necessary on my R500 and use the activation key that came with the R500 to activate that copy of Win 7 if I could not somehow get my OS transferred any other way. So I created a bootable flash drive with the Win 7 Pro 64bit installation files, and used that to install a fresh copy of Win7 on my other 750 GB HDD. That worked fine, no errors. Windows Update worked from the very beginning. This was without Intel Rapid Storage Tech having been installed. At this point I don’t remember if I actually ran Windows Update before upgrading to SP1 or not. The SP1 installation ran normally right from the same optical disk, same DVD, same hardware, only a different type of OS installation. I ran FSUTIL FSINFO from CMD window and got “Bytes Per Physical Sector : “ on the 750 GB with the straight OS installation. I then installed Intel Storage Tech, after which FSUTIL FSINFO yielded “Bytes Per Physical Sector : 4096” At this point I surmise the Lenovo Recovery Win 7 Pro 64 bit OS & the ISO OS obtained from Microsoft differ in some key respects. I’ll submit another report after SP1 finishes installing itself.

  4. ArtFD says:

    SP1 successfully installed itself after 45 minutes of running. Windows Update started working as soon as I got its window open and clicked on the ‘update’ radio button. Now downloading 127 MB of updates. Perhaps the sequence for Win7 Pro 64 bit with 750 GB Seagate Momentus HDDs is (1) restore OS from OEM partition (2) install Intel Rapid Storage Tech (3) install SP1.

  5. SGT says:

    I feel awful that I noticed this problem about 9 months ago when the 750GB drives just came out and I spoke with Microsoft multiple times and they promised me that they’d release a working KB on it. I see that they have not. But installing the Intel RST is the key.

  6. Bonecrkr says:

    Updating the Intel® Rapid Storage Technology driver did the trick for me. Very frustrating problem because there were so many different answers that did not work at all. Apparently you need to have the newer Intel® Rapid Storage Technology driver installed with these new hard drives . All I did was reinstall Windows 7 to a new hard drive on my HP laptop from discs that were sent to me from HP. The discs created a new image instead of installing Windows 7 the normal way. When dealing with images and cloning, you don’t have the option of updating windows components or drivers before installation. Since this is going to be a problem for anyone upgrading their hard drive from an image, you would think that Microsoft would have this solution included in their automated Fix It troubleshooter, but they do not. Microsoft’s website was completely useless.

  7. geoff says:

    I kept getting to the wrong Intel driver. I had to search Intel’s download site for my controller ICH8M-E/M. I went in the Device Manager and looked under IDE ATA/ATAPI controllers and look for the SATA controller. I had to install the file I got from Intel twice before it worked. Now things are running slow, that just might be the file index rebuilding or my next thing to figure out how to fix.

  8. robw says:

    Many thanks for this post! Updating the Intel® Rapid Storage Technology driver did the trick for me. Windows Update is working again.

  9. Sean Flaherty says:

    I need help finding the correct file so that I can “…manually install the latest Intel driver: Intel® Rapid Storage Technology ”

    I have a T400 with an Intel Core Duo 2 CPU T9600 @2.8GHz. I can’t figure out which file to install.

  10. The Geez says:

    That link target keeps changing. Sorry about that.

    Try this search link:

    http://downloadcenter.intel.com/SearchResult.aspx?lang=eng&ProductFamily=Software+Products&ProductLine=Chipset+Software&ProductProduct=Intel%C2%AE+Rapid+Storage+Technology+%28Intel%C2%AE+RST%29

    Then have a look at the “OS” entry for each of the results (mouse over “More” if necessary). Pick the latest one that matches your operating system.

    Once you’ve done that, download the iata_enu.exe and readme files. Follow the instructions.

    The G.

  11. DAVID says:

    Thanks for this post!!! The intel update worked for my T400!!!
    Your post gave me the light on a problem that too many people try to solve in too many different ways! Was a frustrating day, thanks so much that I could land here!
    Grazie! David

  12. Sasa says:

    I solve a problem with Windows Update !!! Thank you very much – T400, W7 – 64
    Problem start after install a Lenovo drivers from System Update .I didn’t know what’s going on – Windows Update not work and I have a mistake:
    DtaStor FATAL: Failed to initialize datastore, error = 0xC8000247
    I use a many MS solutions with nice small tools “funny guy who made something”but without results. Now , all is gone … thank you one more time…

    Hvala,

    Sasa

  13. nycebo says:

    You are a lifesaver. Searched everywhere to get my new HD to work with windows update and MSE…the Intel rapid storage technology drivers did the trick. Thanks.

  14. rafa says:

    You saved my life!

  15. I have to give BIG kudos to The Geez…after nearly a day and a half of research, trial and error, as well as the Microsoft “solutions” (such as detailed and lengthy command line changes) that, well, missed the mark, this was the most on-point, direct, easy to understand discussion of this problem and better yet, solutions that really worked! It started when I wanted to update the OEM 320gb WD Scorpio drive in my Acer laptop to a 1TB SAMSUNG Spinpoint M8 ST1000LM024 so to accomodate digital video and photo files. I had no idea of the new wave of AF drives and the apparent consistent and ongoing problems it was causing to Intel based systems going through HD upgrades/swaps…my MS Update stopped giving the same message, MS Live Mail failed, etc…eventually, after re-cloning my new drive after all the other proposed solutions failed, the first solution offered here above of the Intel Rapid Storage Technology update provided directly on Intel’s website (thanks for the latest links from The Geez) worked. What I did was clone the drive (thanks to Acronis software) and then on first boot with the new drive, the system gives a message to restart since it detects the new hardware. Don’t do it. Wait. Install the Intel Rapid Storage Technology update and when prompted to restart at the end of the install, then you can restart. Upon restart, presto, MS Update works as well as everything else that should. Yes, on the taskbar you will have an additonal icon of the Intel Rapid Storage Technology control which seems like a fair trade to using the more up to date AF drive technology. You have saved the remainder of the weekend and I would strongly suggest to Microsoft to include identifying this issue and your above solution directly on their site.

  16. John Bresnahan says:

    Downloading and installing the Intel Rapid Storage Technology drivers worked for me on an HP P6300f where I restored an image of a failing hard drive to a new one.

  17. Tom says:

    Thanks for the pointer — worked like a charm!

  18. Jonas Dagys says:

    Thanks. It works great.

  19. Ivan says:

    Thanks! It worked for me as well!
    Main difficulty was to ask the right question in Google :-)

  20. Daniel says:

    Spectacular – thank you for your post. Had a Sony Vaio VGN-FW11E with a failing hard drive, cloned it to a new one and Windows Updates stopped working. Dozens of resets, no clue or change… but your solution of installing RST worked first time. I don’t know how you figured that out but I’m glad you did, and even more so that you posted about it!

  21. Don Gateley says:

    Infinite thanks. After days of fighting with this and following all the useless “solutions” microsoft gives in all the sundry places it gives them by all the incompetent people they employ and utilize, this nailed it immediately.

  22. HR says:

    Thanks a bunch. I upgraded from 160G to 750G and noticed the problem when MGA started popping up. Tried a number of things, starting, restarting services following MSFT solutions. This one resolved my headache.

  23. Pego says:

    Tank you very much!!
    You saved me a lot of time and of worries!!
    I have a Sony Vaio VPCF11C5E, and from when I changed the hard disk, I experienced a lot of problems with Microsoft Update…
    A great work!

  24. GregM says:

    THANK YOU!!! …. searched a lot of places and tried a lot of useless things before finding this solution. Worked like a charm!!! Good Karma to you!

  25. Bjorn says:

    Thank you!!!
    Upgraded by cloning my Sony Vaio VPCF12Z1E (F-series) 500 GB HDD to “Seagate 1TB Solid State Hybrid Drive SATA 6Gbps 64MB Cache 2.5-Inch ST1000LM014″. Discovered after two weeks that Windows Update was not working as posted above, neither did Windows Defender.
    Downloaded and ran “iata_cd.exe” (multiple Language as my W7 64-bit Home Premium SP1 is running in Norwegian) from: http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&ProdId=2101&DwnldID=22194&ProductFamily=Software+Products&ProductLine=Chipset+Software&ProductProduct=Intel%c2%ae+Rapid+Storage+Technology+(Intel%c2%ae+RST)&lang=eng
    Rebooted and everything worked perfectly without update issues at all!!
    Thanks again!!!

  26. Ben says:

    That did it for me! Thank you!

  27. Nate says:

    Mr Geez, you are a God among men :-) Thank you so much for sharing your insights with the wider Internet community. After the hard drive in my ASUS UL30 (from ~2011) crashed for good, I replaced it with a brand new Seagate and restored Windows 7 from the factory image that Asus provided with the laptop. After restoration, I discovered that Windows Update refused to fetch any updates, even though the corresponding service appeared to be running without any trouble. Installing the iata_enu.exe file (as linked to by Bjorn ) did the trick!! Thank you!

  28. Simon says:

    Odd… Apparently my computer does not meet the minimum requirements to install this product.

    Brand new install of Asus H87M-Pro mobo, with the same Seagate SSDH 1TB Bjorn has.

    As a short term work around I have uninstalled IRST.

  29. Zach says:

    This seems to be the place where people are posting their 4K drive woes, so I’ll post my own problem and solution here – had a lenovo x200 tablet with a failed 750GB drive, so we replaced it with a 1TB – however, the 750 was standard 512 byte blocks, the new 1TB drive was AFD.

    Numerous clone attempts later (yes I know, cloning off a failing drive – bad idea, but whatever) and the user sent me the drive from his X201 tablet instead, which was already a 1TB AFD drive.

    I cloned it, and of course the first thing I did on the newly-cloned drive was run the fsutil to tell me “bytes per physical sector” which until this time had been “not supported” all the other times. This time it was 4096! success! So I started removing the X201 drivers and installing the X200 drivers, etc etc…then suddenly windows update stopped working again. My heart stopped when I saw that I was getting that teeth-grinding error that we all saw at the top of this original post.

    I couldn’t find where to install the Intel RST drivers (installing the 16MB file says “not compatible with this system” so instead I hit the devmgmt.msc and went under “IDE ATA/ATAPI controllers” and then saw the Intel chipset driver in there, the storage controller. i saw that it was using the iastor.sys driver, (and it wouldn’t take the newer one that the author linked to) so instead I told it to try the 2006-era microsoft driver, instead of the Intel one. (this is under the “update driver” then “browse my computer for driver software” then “let me choose which driver” – that list had both the Intel driver that I must have installed while doing all the updates (that ruined everything) and also the original MS driver – I picked the latter).

    I rebooted the computer, and sure enough, I had 4096 byte physical sector size listed again in FSUTIL.

    For whatever reason, the driver that was installed while I was uninstalling/reinstalling drivers wasn’t compatible with the computer, but the ancient Microsoft driver was.

    Worth a try, everyone!

    • B says:

      Zach’s approach also worked for me. A cloned 1.5TB HDD replaced a 325GB HDD and produced exactly the same problem as at the top of this tread.
      My Intel Core 2 system wouldn’t take the RST driver so I tried what Zach does in his 4th paragraph and my post-clone of Windows 7 system Drive problems with Windows Update and Indexing are solved.

      • Adam says:

        Thanks for this solution. The same worked for me. Have replaced original hard disk with WD 1 TB one in my ‘old’ Acer Travelmate 6292 running Vista. After cloning Windows Update was broken. Which I noticed only after a couple of weeks. Found this post and tried to update the Intel drivers. However, none appropriate for my system restored the Windows Update. Going back to the Microsoft driver ‘Standard AHCI 1.0 Serial ATA Controller’ from 2006 and subsequent automatic install of some additional elements Windows Update worked perfectly again. Not sure what the impact is on speed of communication with the hard disk though.

  30. Hans says:

    Hi,
    it happened to me. Thanks for the solution.
    In short: Asus N71jv notebook, Win 7 home premium, 3yr old, Seagate 500GB HDD crashed. Replaced by a WD 500GB drive and used Clonezilla to restore a month-old image. Ran fine except for Windows Update. Searched a lot, tried different things without luck. Was pointed in the direction of faulty activation with MS, MS pointed me to Asus because of OEM, Asus pointed me to Clonezilla, …
    I found this thread and DL-ed “f6flpy-x64.zip” from Intel RST, unzipped, opened Device Manager and updated the driver for my Intel SATA AHCI Controller. Rebooted. Problem solved.
    Thanks ever so much.

  31. Steve Christensen says:

    Many thanks for this thread, as it help me solve the issue. 2011 Dell XPS-435 desktop, on which I upgraded from a 1 TB to 2 TB boot drive last month – only to notice after about a month that Windows didn’t seem to be running any updates when I shut down on Wednesday any more. I tried lots of other things to get Windows Update to work, and based on this discussion I finally downloaded an Intel RST driver called “iata_enu” that did the trick.

  32. BtotheP says:

    That has fixed the issue for me as well a few months ago. But I just started getting the same problem again. I did notice a couple weeks ago that the Intel RST was not running and has not been for a few weeks. I thought maybe it wasn’t needed after a cpu upgrade. Maybe not the case. I will try to update it or reinstall it to get the issue resolved again.

  33. Jim says:

    Many thanks for the information above. It fixed my problem as well with Windows Update after a hard drive replacement.

  34. MIDAS says:

    So glad I came across this post!

    I also ran into this issue after “cloning” a WD HDD to a Crucial SSD on a 64-bit Win 7 Acer Aspire 5738ZG laptop – the “Check for Updates” button did nothing when clicked – no error message – nothing!

    In addition, I found that downloading anything through IE (version 11) also failed!

    However, installing the “AHCI: Intel® Rapid Storage Technology Driver for Intel 6 Series Chipset-Based Desktop Boards” (STOR_Win7_8_11.7.0.1013_PV.exe), and then restarting the laptop did the trick for me!

    Once again Windows updates are working, as indeed are downloads in Internet Explorer!

    Thanks so much for this article!!! It’s saved me a LOT of time/frustration!

  35. John says:

    I’ve been struggling for about a week trying to update my old Netbook HDD to something that was bigger – 750GB in this case. Hopefully, my experience and how I resolved it, can help you avoid a lot of pain.
    It all started going pear-shaped once I had re-installed, from the manufacturer’s install disks, windows 7 onto this new drive. Once I’d got into the brand spanking new Windows install, I tried running Windows Update – well, it reported that Windows Update wasn’t running. So I checked in the Task Manager | Services to see if it was – it appeared to be but I restarted it anyway. Still no go!
    So I went online and tried to find similar instances of problems like this. A quick search turned up a problem with Advanced Format Drives. This sounded promising, so I checked the Microsoft support knowledgebase for this and came up with KB982018 “An update that improves the compatibility of Windows 7 and Windows Server 2008 R2 with Advanced Format Disks is available” – unfortunately, this wouldn’t install because Windows Update wasn’t running! Catch-22!!!
    Could my installation be bad? I re-installed – still no go. I went to the manufacturer’s website and downloaded all driver & BIOS updates. I installed them all, rebooted and still had the problem. :-(
    I called MS support and they suggested installing from a SP1 iso file of Windows7 (Home Premium in my instance) – I downloaded this but, after years of using the Netbook, the Windows Product Key had all but been rubbed away – I could discern only about half the characters. :-(
    This is eventually how I succeeded:
    * Is it the install media? I installed it onto a smaller drive I had around and WU worked fine. OK, media is OK.
    * So let’s install SP1 and the KB982018 fix onto the smaller drive. All good.
    OK, now I have a working installation but on a smaller drive.
    So I installed all the downloaded drivers from the manufacturer. Reboot – all good still.
    I then used “Backup and Restore” to create a System Restore Disk – BTW. this will fit on a CD. Still in “Backup and Restore” I then created a System Image file, including ALL of C-drive. After successful completion I shut down the PC.
    I then replaced the 750GB disk and booted to the System Restore Disk. Here is the important bit – I loaded the updated drivers from the manufacturer (I did both chipset and HDD controller drivers but this may not be essential) BEFORE restoring. Previously, the box to enable formatting of the disk was greyed out; after loading the drivers, this was enabled and I dutifully ticked it. This enabled the drive to be formatted by windows using these drivers before doing the system restore.
    System Restore completed, I re-booted and Windows Update is now happy. I just need to re-size my partitions to make it work for me. I hope this helps some of you who may be struggling with this same issue.

  36. Utility Account says:

    The “intel driver solution – sp47845.exe” worked for me as well after using clonezilla to clone a Win7 drive that gsmartctl suggested could be failing. What I still don’t understand is why it worked (I never had these drivers before) unless the newer disk I used (it was exactly the same size and from the same manufacturer, just three years newer) somehow required them.

    If so, I would have expected the OS to warn me of this when it recognized the new disk, installed drivers and asked me to reboot – this during the first boot after cloning. But we end up having to rely on a third party vendor to solve issues related to simply replacing a disk with a clone. There has to be a trouble free way of managing that pretty common task.

  37. John says:

    Been fighting this as well. I upgraded an old Dell Inspiron 1525 laptop with an SSD. Uninstalled the Intel driver and installed the standard AHCI 1.0 driver that came bundled with Vista. Windows Update works like a charm.

  38. Al says:

    The install of the RST driver worked perfectly on my XPS M1530. Doing an update right now. Thanks!

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