Sounds like the battery is bad. I have an M5A99x, I think they are the same BIOS. I have changed settings manually and through the AI suite and never had a problem, even without setting the changes to one of the profiles. If you have a volt/ohm meter, you could easily check the battery voltage. The clue is your clock and date returning to default. Maybe the battery is just not seated properly. I assume you know the battery is between your first and second PCE x16 sockets.
I presume you are saving the changes as you exit the BIOS!