I'm trying to think back a few months, I believe my Atlantis was doing the same type thing. My issue was caused by the "reset completed relay" down on the motor board. It had gotten out of adjustment somehow and it would not release. I adjusted the amount of friction on the plate and fixed it. This works sort of like a game over relay.

Thinking a bit more about it, I actually adjusted it so that the armature plate was closer to the end so that it would trip easier. It had nothing to do with the switches but the movement of the armature. Sorry if I'm being too confusing....Hopefully your Atlantis working. Great game!