It sounds like a typical switch matrix issue. Most likely you do still have a diode or capacitor acting up. You've identified at least 3 switches that are acting up , there's possibly a 4th one somewhere. You mention the ball being drained while still in play , this means switch 17 , outhole reflex is considered close for this to happen. You didn't say if you can replicate this easily or if it seems totally random. If it seems random , this means another switch must be closed. I'm not familiar with Catacombs at all , but from what I just saw online , there are 2 lock balls that carry from game to game.. So theres's a good chance that these are involved in your issue. Does the drain happen when either of these 2 balls are locked ? A shorted,reversed or missing diode can cause such issues, the machine seeing the wrong switch closed when pressed. I have identified a few switches that could be involved. Do you have a multimeter to test both the switches and the diodes ? I would start by testing the following switches and their diodes and after that their wiring (check the wire color). Was this machine working properly and then issues happened ? Or did you pick it up in this state ?

Edit : If diodes and switches are ok , then you'll have to check the capacitors (if any) associated with each switch. I *think* people usually lift a leg of the capacitor to test the switch without the capacitor attached, but I'm not 100% sure on that, others will have to chime in on this.

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