Quoted from wdennie:make sure the big asic chip is pushed (seated) in all the way.
Right flipper: everything? even flipper optic board?
sounds like a dirty optic.
Yes, I believe start at the optos for the flipper issue. If you clean the optos and nothing changes, you can move the flipper opto board to the left side to see if the problem then starts on the left flippers, then you know its optos. As for the factory settings issue... thats a weird one. The ASIC could be the culprit. Some De-Oxit spray could help those connections, as well.