My suggestions:
- Repair your hard drive and permissions.
- Backup your hard drive or at least backup your Home folder.
- Erase the hard drive.
- Reinstall OS X.
Repair the Hard Drive and Permissions - Lion/Mountain Lion
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.
Repair
When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported then click on the Repair Permissions button.
Clone Lion/Mountain Lion using Restore Option of Disk Utility
1. Select the destination volume from the left side list.
2. Click on the Restore tab in the DU main window.
3. Select the destination volume from the left side list and drag it
to the Destination entry field.
4. Select the source volume from the left side list and drag it to
the Source entry field.
5. Double-check you got it right, then click on the Restore button.
Destination means the external backup drive. Source means the internal startup drive.
Install Lion/Mountain Lion on a New HDD/SDD
Partition and Format the hard drive:
1. Select your internal hard drive (this is the entry with the mfgr.'s ID and size) from the left side list. Click on the Partition tab in the DU main window.
2. Under the Volume Scheme heading set the number of partitions from the drop down menu to one. Click on the Options button, set the partition scheme to GUID then click on the OK button. Set the format type to Mac OS Extended (Journaled.) Click on the Partition button and wait until the process has completed. Quit DU and return to the main menu.
Reinstall Lion/Mountain Lion: Select Reinstall Lion/Mountain Lion and click on the Install button. Be sure to select the correct drive to use if you have more than one.
Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.