I open the command line and put this in that machine. Alter it to match the drive you suspect, exit, reboot and then wait for it to finish.
And did I mention you should backup what you can't lose first?
-> CHKDSK /x C:
Answer yes to run it at the next boot.
I'm using xp pro sp3 and after im done typing my letters I go to restart to go to my linux install and just after the windows desktop closes but just before you see the "logging off" text, there was a message that popped up saying "the system filestructure is corrupt. check file system with check disk" but it really didnt allow me to do anyhthing as it was already shutting down.
Well I logged on later and nothing appears corrupt.