What is the error that it gives?
Does it let you view diagnostic and repair details after the automatic startup repair runs?
If so, does it list a ROOT CAUSE?
Here is an example...
Root cause found:
Registry is corrupt:
Repair action: Registry roll back
Result: Completed successfully. Error code =0x0
Time taken =7722 ms
That would give us a clue as to the next step to take.
EDIT: Also, I still need to know "What happened before the computer stopped working? Did you have a virus or any errors?" Is there a particular reason that you think it is a registry problem? Sometimes the main drive with the directory \Windows\system32\config is not C: in the recovery environment so the error that you could not find the directory may have been because you were looking at the wrong drive, not necessarily that it is missing and causing the computer not to boot.
Edited by James Litten, 19 October 2012 - 09:50 PM.