Typical ST TNG problem
The trough will be slightly pitted, and what happens is that at least 2 - 3 balls will be in the subway before the game will work properly. So there CAN be 2 balls in the trough - which is fine, but, there will be a section of the ball trough that is so worn, that the timing of the first ball into the catapult switch is detected, but the second ball in the trough has not moved into the area of the first ball "in time" - so the game spits out the second ball. You can see this for yourself when you remove the apron and look down into the trough - the first ball is served and the second ball has not moved. There is no third or fourth ball to "push" the second ball.
I fix this issue by removing the trough, dismantling all the parts and then filing the trough until the pitted area is smooth. Re assemble and test.
I know I've seen this problem twice - one fix was the optos, the other was the pitted trough.
Make sure the target at the top of the playfield is working. The game gets VERY confused if it does not reset at the start of each ball.