Not to familiar with this game but when the ball goes into the left or right scoop and another ball pops up in the shooter lane that could mean the ball in the scoop is being held for start of multiball mode,also that means that ball in the scoop is registering. But put the game in switch test and drop a ball in the scoop and make sure it's registering properly on the dmd screen.. could be a flakey opto in the scoop likely the transmitter opto(one with the bulb).
The ball not popping back up upon start up a new game could be the coil or the coil sleeve to that scope.. coils dont go bad could need cleaning and the coil sleeve to that coil may need cleaning. Remember when game is in test mode and hi power is on the coils have more power because your testing them one by one. During gameplay they are not that powerful.

Check the menu, there is an adjustment to have a ball in queue on the right side. I turned it off on mine because when you first power it up the cpu loses track of the ball.

Yeah, I did the same thing. I think it's this adjustment:

who_dunnit_disable_staged_ball (resized).png