Quoted from javagrind888:
I figured it out! So I remembered people earlier saying if any switch was hit on the lower playfield, the gate closes. Days ago I had a leaf switch registered as stuck closed. It went away on its own without me adjusting it, I just kept a mental note of it in case it happened again. I adjusted it anyway and the problem ceased! It must have been touching when the flippers vibrated the machine. Odd it didn't happen during the "bang on the playfield test". Anyway, there it is. Hit the ship three times in one game.
Glad you got 'er figured out!
I wish they chose to use a latching relay mechanism but I guess the thought was that 1 more coil is 1 more point of failure. I also wonder if there's a great risk of a tiny hold coil even burning out if just left on rather than software disabled... but I'm no engineer.