Two thoughts come to mind. One is switches that are gapped too closely. However, you said that you checked them. Did you check the start button as well?

The other thought is a shorted diode. Go into YouTube and search for TerryB pinball shorted diode switch matrix. He has an excellent video explaining how to diagnose. Basically, you want to look for instances where two switches are closed, and pressing a third switch triggers a fourth switch. If all four switches form a rectangle on the matrix then it is a shorted diode or a short bypassing the diode.

Let me know if you can’t easily find the video, and I can find and post.

Switch matrix issues are always so tricky to nail down. In self test, there may not be closed switches because all are open, unlike when you are playing the game. Try to figure out when it happens while you are playing. Are drop targets down, other switches closed, etc.? I often find on the older games, it is easier to diagnose by playing with the glass off and trying different configuration of switches to see what happens.

It could be that the EOS switch for the flipper is in the matrix even though it isn't shown. I don't know, i'm not familiar with the particular game.

It could also be that the vibration from the flipper is triggering another switch that is gapped too closely, and that completes the rectangle indicating a shorted diode. Try banging around the playfield with your fist and see if any switches fire when they shouldn't.

Also, it could be nothing is wrong with a diode, and you have a short to ground somewhere. You could inspect all switches, including on the flippers and make sure no wires or lugs are pressed up against lamp sockets or other metal fixtures. I find shorts to ground to be the most difficult. It is like looking for a needle in a haystack.

Lastly (for now), it could be a board problem. The way to check for that is in switch test mode, you disconnect the connectors in the back box that correspond to the switch matrix and jump the pins to try to trigger the switches one at a time. If all trigger correctly, then it is not the board, and it is something on the playfield. Again, I don't know enough about this particular pin to advise you on which connectors, and I don't want to mislead you. From the diagram, it looks like a combination of J2 and J3, but I don't know for sure, and I'm not sure why there are two in each column and row. Perhaps ask someone else who owns the game to confirm.

On the topic of how the flipper might be causing issues here, make very sure that any diodes soldered on the coil (or on the board the flipper coil is triggered from if they’re not on the coil itself) are good and connected well at both ends. When the coil is released it generates a high voltage spike in reverse that can cause all sorts of havoc without the diode, whose job is to short that spike back through the coil rather than the rest of the circuitry.

Typically, you need to desolder it to test. However, technically I think if the switch is open it counts as the same thing. One side should measure infinite resistance and the other side should allow current through.

Nice! Congrats.