Sorry for slow reply, its been a busy day, snowing like crazy down here. Sorry for the confusion, let me clarify. The playfield flippers themselves work fine, while playing the game. However, when navigating through the menus, the right flipper button does nothing. Its supposed to select/change options, like changing high scores, switching to freeplay, etc. but it does nothing. The left flipper button works fine, allowing you to go up/down options but that doesn't do any good, without being able to change anything.
The playfield flippers don't fire, while in the menu, but i'm pretty sure they aren't supposed to. We have a que ball wizard that uses the same Gottlieb 3 setup. It's in 100% working order and it doesn't fire the playfield flippers, when navigating the menu. I switched the sensor boards between the two and nothing changes, in either, so i know those are good.
Going to recheck the wires/connectors again, in case i missed something. Other than the menu/flipper problem, game works pretty good. Thanks for the help so far.