Well I tried messing with the dipswitches for three games; frogger, burgertime, and donkey kong. With frogger, changing the cabinet dipswitch from upright to cocktail worked perfectly. P1 joystick controlled P1 and P2 joystick controlled P2 and the screen didn't flip. Setting burgertime and donkey kong to cocktail also enabled P2's controls, but it inverted the screen. ---smurfy---!
Also, I'm running version .135. Maybe a newer version will be able to do this? In the mean time, I'm going to have to go the PBJ route.