Id' strongly suggest that you'd backup your system (if it's not already done) and then you should file system check your hda drive.
For this, you have to boot your machine in single user mode or go to it from your normal operating level.
Type init 1 after warning users :-).
Halt the grub menu by hitting the space bar when the countdown comes.
You can then choose 'e' when the menu displays; to edit the boot paramters, select the line that starts with kernel, for the kernel you want to boot. Go to the end of the line and type single as a seperate word (press the spacebar) and then type single. Press Enter to exit edit mode. Back at the GRUB screen, type b to boot into single user mode.
Once there, un-mount the partition that's causing you grief, then:
>fsck -y /dev/hda 'or you can specify the partition if you know it.
It might take a while depending on your drive space.
Hope this helps.