This was one I hadn’t seen in a while to be fair, and caught me a bit off guard, but it is well documented.

Cloned Windows 2008 R2 virtual machine fails to boot with the error: autochk program not found – skipping AUTOCHECK (2004505)

What was interesting for me was this happened on ESXi 5.5 hosts, which the KB article doesn’t mention, but the VM hardware level was v7, so my guess is that’s how its correlated.

So the KB mentions doing this:

If these steps do not resolve the issue, try this alternate workaround:
  1. Power down the source virtual machine.
  2. Boot the virtual machine using the Windows Server 2008 R2 .iso file.
  3. In the Installation Wizard, select Repair your Computer. For more information, see the Microsoft Knowledge Base article 2261423.

    Note: The preceding link was correct as of August 18, 2011. If you find the link is broken, provide feedback and a VMware employee will update the link.

     

  4. Select Command Prompt.
  5. Run these commands in the specified order:

    diskpart
    list volume
    select volume 1
    attributes volume
    attributes volume clear nodefaultdriveletter

  6. Restart the virtual machine after removing the mounted .iso file.
  7. Clone the virtual machine again.

Now the VM I am wanting to clone is up and running and I dont want to take it down. So I did as follows:

  • I created a clone of the VM with no customisation
  • Mounted the ISO image on the newly cloned VM
  • Booted it up and ran diskpart exactly as described
  • Then did a clone of the clone, this time using the customisation script to sort out the SSIDs get, and it worked perfectly.

I then just binned off the interim clone!

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