Have you run error-checking on your hard drive? If you havent, I'd start there first. Its as simple as right-clicking on your hard drive going to Properties, then selecting Tools Tab, and then Check Now. It may tell you that it will check on the next startup, and agree with this and then reboot your computer and let it go through the error checking of the checkdisk process. If the drive is healthy it will get through this pretty quickly. If it finds problems it will try to fix the problems.
I have seen this happen before with a drive that has its file tables messed up so hoping this will be the fix for you.