I'm not sure I can be of much help, but can you confirm the wiring is correct on the flipper coils: Cathode (Banded side of diode) is Power and Anode is the trigger/drive?
I don't know if a bad diode on the upper coil would cause this or not. I *think* that a bad transistor on your power board would cause the coil to activate on power up, but you might want to check the transistors on the 50v/Coil area to see if they are good.