Make sure you have a current backup. What is the SMART status of your hard drive?
The best things for repairing directory issues on OS X is Disk Warrior made by Alsoft. I would suggest you pick up a copy of that if you can.
If your hard drive checks out OK and you want to try out something that's free before buying Disk Warrior, you can boot into Single User mode and user fsck (file system check) to see if it fixes your problems.
1. Reboot the computer and hold down command (the apple key) + S, this will load a minimal version of OS X and take you to a command line.
2. Type 'fsck -fy' without the quotes and see if it can fix he error. Do it a few times until it doesn't give you the error any more. If this can't fix it, then your next option is Disk Warrior. If that can't fix it, then your last option would be an erase and install.
Good luck, remember to keep us posted.