Try this:
http://www.techtv.com/callforhelp/ma...409933,00.html
The application is called Drive 10. Boots from the CDROM, and will run checks of the hard drive. The link is to an article about the app.
If you hear the hard drive "clicking" then I would think that the problem is with the hard drive, and not with the filesystem.
Is the problem with the same file(s) all the time?