Go to Disk Utility, and do a Verify Disk. You can run that without any risk since it's just looking. If it finds errors, then you need to boot from your install disks, or a bootable external HDD and run the Repair Disk option.
I don't actually know that is the problem, but the verify disk is a painless and risk-free diagnostic tool. At worst, it will eliminate directory problems as the culprit. Good Luck.