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Cloned Drive Missing File; Source Drive Damaged

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Using Acronis True Image Home 2009.

On this one Windows XP Pro (fully updated) computer, every time I clone the hard drive (C and D partitions) the cloned (destination) drive produces the following message on start up:

Windows could not start because the following file is missing or corrupt:
\windows\system32\config\system
You can attempt to repair this file by starting Windows setup using the original setup CD-ROM. Select 'r' at the first screen to start repair.

I've checked the disk and no files appear to be missing (and indeed, that message refers to a directory, not a file).

At the same time, the source disk incurs some damage from the cloning. When I restart the computer with the source disk, I think Chckdisk runs and fixes a ton of errors -- bad indices, bad files -- it goes by too fast to get them all, but I think it's in the scores or even hundreds. Once done, the computer runs just fine.

I'm at a loss to figure out what's going on. The drives appear to be okay (although I am going to run chckdsk on them individually soon).

Any assistance would be greatly appreciated.

Key Components:
Motherboard: Asus M3N78-VM
CPU: AMD Phenom X4 9850 (not overclocked)
RAM: 4 GB
Video card: ATI Radeon X1650 (PCI-Express)
OS: Windows XP Pro SP3, fully updated

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Instead of Clone, try doing a Backup (Image) then restore the Backup to the destination drive. And do this using the bootable Rescue CD.
You will need a third drive to hold the Image unless you first store the Image on the destination and if the source has enough room, move the Image over to the source before doing the restore.

Daniel,

Did you try the cloning procedure when booted from the TI Rescue CD
This procedure below is called a Reverse clone:

Remove the source disk and place it in an alternate location--such as an external enclosure.
Install the new blank disk in the same location as the original source disk.
Perform the cloning procedure when booted from the Rescue C.
After cloning, be sure and remove the source disk before first bootup following the cloning.

Old drive can be attached later after the clone is functional.

Any hidden or diagnostic partitions should be created in the same size as original.

Thanks for the idea. I'll give it a try.

The underlying question is why is this phenomenon suddenly occurring after all these years of the cloning procedure working without any difficulties?

I'll let you know if this works. Thanks again.

Rather than go through all these macerations, on a hunch I uninstalled Acronis True Image Home 2009 and installed the 2010 trial. Acronis now clones the drive just fine. What a relief!

Thanks for your suggestions. I guess I'll just have to buy the new 2010 -- which I'd have to do anyway if I upgrade to Windows 7 (which is questionable since Windows 7 prevents the pan and scan virtual desktop -- aka "overscanning" -- that I have come to depend upon).