You could possibly have a failing hard drive or bad hard drive cable. OSX is very tempormental when it comes to bad blocks and starts to act very strange. I would make sure you have your data backed up and then do the following:
Restart the machine and as soon as you push the power button hold the Command and S keys at the same time. You will now boot into single user mode.
Once things are done and you are into single user mode, type the following:
See if that fixes it. Keep any eye out for errors as well. If it finishes without issues, then I would do a surface scan on the drive (after backing up your data as a surface scan can kill a failing drive or make it worse).
To exit single user mode, just type reboot.
Are you still using the same hard drive as before? That is bad ju ju waiting to happen. Replace the hard drive if it was beginning the fail. You are just asking for trouble. Also be SMART and use an external drive as a Time Machine backup. Keeps you out of trouble.
Edited by Lord Xeb - 9/13/12 at 4:37pm