Virus/spyware/malware or corrupt harddrive I'd think.
Try safe mode, press F8 before the windows boot screen, but after the BIOS one. Once you're in safemode scan for malware with some kind anti-virus program, some free ones are: AVG Free, ClamAV, Spy-Bot Search and Destroy, Lavasoft Ad-Aware, etc... Go to download.com if you're having trouble finding any of these.
Then, go to My Computer, right click your HDD, properties, and somewhere in there you can scan the disk for errors, do that.
In Windows it's also good to defragment your harddrive like once a month, but if you do it too often it isn't good, I think you're not supposed to do it more than once a week...you'd have to look that up though.
If your HDD is corrupt then re-install to see if it's just the partition messed up or if the actual HDD is...and if you have a lot of malware you might just want to re-install windows anyways...or some other OS.