i'm reading your thread and i had exactly the same problem and it was driving me nuts.

on my machine (space invaders) i did 3 things and one of those fixed the problem and still working great .

changed the chip at u8 (scm5101e-3).
changed Q5 transistor pnp (mps-3702) i saw one of the legs had a small crack, not completly broken.
unplugged all the connectors on the mpu board and checked every wires on those connectors. i doubt it was the problem.

did work for me, could work for you, hey you never know.

bally_mpu_board.JPG