You might have the Windows File Protection problem that I have seen in the past. We downloaded a utility from Microsoft to clean up the problem... unfortunately I do not have it here with me, but it went through the system and cleaned up a bunch of issues.
Perhaps it is time to run some tests on F: I am guessing you are Win 2K or XP. Open up the Disk utillities, and run a checkdisk on the system. See if finds problems. I am also wondering if you have NTFS on F and if the permissions there got messed up.