Have occassionally had this on copying boot drives to new hard disks. Often difficult to fix - there are many proposed solutions, most of which dont work for me.
I came across some mention of this key - HKEY_LOCAL_MACHINE\SYSTEM\MountedDevices - and had a look. I did this offline by booting from the windows recovery disk, opening cmd.exe, typing regedit and then using regedit to load the hive I was interested in. To do this go to a key and click on File on the menu. Then navigate to the hive you want. For this it will be X (where X is the drive letter that your normal boot (C:) drive appears as in the recovery disk drive list - it wont be C:. The hive is in Windows\System32\config and is called system. Load this and give it a name - anything will do.
Then in this mounted key navigate to MountedDevices. I suggest exporting it at this point in case of a fubar. Have a look for a key named \DosDevices\C: - there should be one. Its data type is REG_BINARY. Its data value will be 12 pairs of hexadecimal digits. The first four pairs are the drive signature. The last 6 pairs are the drive offset. There will be another key with a name begining \??\Volume{some long number} with the same data value.
When I looked I had two entries with the same value for \??\Volume{some long number} with the same drive signature and different offsets, one corresponding to 3Fh and one to 800h (see http://diddy.boot-land.net/firadisk/files/mounteddevices.htm).
I thought playing around with these would fix the problem. It didn't but I guess it might have done if this pair of conflicting offsets had been the cause.
As it sounded like a likely culprit (boot starts -> faulty mounteddevices directs boot to the wrong or a nonexistent drive or the wrong offset -> boot fails etc.) I looked further.
In the windows recovery environment registry, the key for my C: drive in mounted devices (actually E: in the recovery environment) had a completely different drive signature. I edited my loaded hive entries - \DosDevices\C: and the matching \??\Volume{some long number} entry to have the same drive signature and offset as shown for that drive in the windows recovery environment.
Bingo - normal boot.
So, at some point in the drive copy the drive signatures had been messed up - dont know why - but this joins the list of potential solutions for the dreaded "autochk program not found - skipping autocheck" cyclic reboot.