One of my nightmares over the last couple of years - it happened again yesterday. This was what greeted me when I started my Windows XP yesterday:
"One of your disks needs to be checked for consistency"
This only occurs on the C: drive. Windows will 'fix' this problem alright, via a 'CHKDSK', but always will some files deleted. The only thing I could do is to restore the deleted files from backups; which is a laborious task since Windows doesn't actually tell me the directories/folders the deleted files were from. At the back of my mind, I always have this feeling that one of these days, some essential system file will get messed up real bad rendering my PC unbootable.
Googling didn't help much as I could not find anything specific to this problem.
A Lead?
It's only a hunch, but my suspicion has always been on the Avira Free Antivirus software for it is the only application that modifies my C: drive regularly via its automatic updates. But I have never had any concrete indications ... until yesterday (well, at least I believe it is so).