If you have needed to do a restore several times, then it seems you have been experiencing a number of problems, including the one you detailed.
I know it is not a very convenient solution, but I think after experiencing the problems you have, the best idea would be to reinstall the operating system. This should eliminate all your problems (unless you have a hardware issue).
If you decide to go ahead to reinstall the operating system, make sure you first backup all your important data, and ensure you have the installation files for your programs, which you will need to reinstall after reinstalling the operation system.
Doing this will give you a totally "clean", uncluttered system, with the added bonus that it should run faster.