Sounds like you might have an issue with the hard disk. You can let windows scan it for you if you boot off of the windows install disk.
(Link below.) When it shows you the install button, there should also be a repair option. If you go through the process you will get to a screen that will let you open the console.
Open the console and run: chkdsk /f <drive letter>
This post has some screen shots, page 7 has the options I am referring to:http://pcsupport.about.com/od/toolsofthetrade/ss/windows-7-startup-repair.htm