Quoted from JoshODBrown:

I've tripped across this maybe-a-bug twice on the new code, i am about 50 games in on the latest version. I am not sure the exact steps to repeat, but in code .89 on the pro... it seems having two mini wizard modes at once, like Battle over Endor, and Destroy the Death Star, in two different games I've stacked other multiballs during those split mini wizard modes (like Tie Fighter and/or Hyper Drive) and then some interesting things end up happening.
The double posts and the upper loop post end up going up at some point in all the craziness (usually i end up getting all 6 balls in play using the add-a-ball), because it thinks a ball is trapped in there, but there is no ball in there (timing of the posts rising must have just missed it). Then one of the balls from my multiball ends up going in the right mystery scoop, and it doesn't realize its in the scoop, so doesn't spit it out.
At some point i am down to one ball left, basically i can't shoot the loop shots (because there is no captive ball to trigger the opto to drop the posts), and it doesn't want to spit the mystery scoop ball out either. I ultimately end up draining the one ball I still have control of and then the loop posts drop, which then ends my mini wizard and multiball modes. Then I wait for ball search to release the mystery scoop ball, and everything goes back to normal single ball game play. I'm pretty positive there is no switch problem in my scoop, since ive shot it in there a hundred times in other non stacked multi balls and regular play and never had a problem. Ive stacked mini wizard modes with the other multiballs lots, and it doesn't always happen, but there is some combination of things happening to get this bug and both times its happened it was during the crazy stacked multi balls.
I am thinking the false/phantom ball trapped in the loop maybe is causing the mystery scoop problem . Perhaps the game is keeping count of where the balls are and is counting a certain number in the trough, and then assuming there is a ball in the loop, plus the ball that is still in control hitting various things and doesn't fire the right scoop as a result. I'll keep trying to reproduce this one, but just thought i'd mention it here in case someone else has noticed something similar.
Both of these games I blew up the score pretty crazy. 1st game where it happened was 6.9 billion, and my other game was like 4+ billion.