This may be resulting from a pre-existing problem when you upgraded to Snow Leopard. In any event I think you should perform major surgery which means you need to have a good backup to start. Try the following:
Install or Reinstall Lion/Mountain Lion from Scratch
Be sure you backup your files to an external drive or second internal drive because the following procedure will remove everything from the hard drive.
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
Erase the hard drive:
1. Select Disk Utility from the main menu and click on the Continue button.
2. After DU loads select your startup volume (usually Macintosh HD) from the left side list. Click on
the Erase tab in the DU main window.
3. Set the format type to Mac OS Extended (Journaled.) Optionally, click on the Security button and set the Zero
Data option to one-pass. Click on the Erase button and wait until the process has completed.
4. Quit DU and return to the main menu.
Reinstall Lion: Select Reinstall Lion/Mountain Lion and click on the Install button.
Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.