There's a switch in the shooter lane where the ball sits that's supposed to tell the game that there's a ball there (switch #18 on page 2-42 & 2-43 of that manual). Go into switch test in the diagnostics menu and manually engage that switch using a ball (don't use your finger, it's squishier than a pinball and can activate a switch much more effectively than a ball). In switch test, it should indicate that switch is being activated on the screen when you put a ball there, as well as any other switches currently being activated (eg., the opto switches in the ball trough if there are balls in there).
Alternatively, you can go into the solenoid test described on page 1-15. Also on that page, it states that "In order to operate the tests that use the +50v or +20v circuits, pull the interlock switch button out. The interlock switch is located on a bracket in the coin door opening". Set the solenoid test to "repeat mode" and cycle to solenoid #09 for the trough eject. Have the playfield in it's normal resting position with all the balls in there. See if you can get a glimpse of the ball behavior when this test is running (specifically, the first ball being ejected while there would be one ball already in play on the playfield, simulating the conditions of starting this multiball). See if the trough eject mechanism is causing the other balls in the trough to roll back up a little bit. If the last ball in line is pushed back up to activate the opto switch behind it, the game can think there are more balls in the trough than there are and prematurely eject another ball.
However, if this were the problem, I would think that it would occur any time a ball was served.