Pretty sure I had something like this happen when one of the small caps on the switch matrix lines was bad. I'm not sure if I ever logged that repair anywhere. May have been C32 (390pf) which is the cap on the SELF TEST SWITCH line. I think it was happening when I'd hit a switch, but it may have been random.
Does it still happen after you start a game if you unplug J3 (cabinet switches & self test)?
To rule that cap out you could try desoldering one lead on the cap to break the connection and see if it still does the same thing.