When I hear of problems of this mech, I tell people to make sure they have the most up to date rom. Everyone should attempt to acquire this anyway for any game, but I found with mine many jaw mech issues were fixed with the latest rom. I would start with that.

The three switches may be working when tested, but make sure they are all making good contact when the ball is in there, and the ball in fact is able to activate them. I'm guessing this is a problem with the closest switch to the kickout.

What I would try is figuring out which switch is the last one, in other words, the last switch to have the last ball when MB starts. When it only spits out two, instantly go into test menu, and switch test and see if that switch is in fact registering as closed.

There is a test in the menus that will tell you what the fault is, it is test 15 the lockup test, select the second option and close the door and throw balls in there, it will tell you the problem