The hunt continues, tonight I decided to play while video recording to catch the problem in action. I finally caught the issue. If I start a 2 ball multiball from the lower lock, when only one ball drains it thinks the players turn is over and counts down bonus and changes to the next player.
Then, when trying to replicate this issue. I found that sometimes when I lock a ball in the lower lock and it kicks out another ball... for some reason the locked ball wont release. But after I drain, then the locked ball releases and continues the same players turn just like a locked ballsave.
Also, possibly related... I dont think the gate for the upper lock is working properly. I feel like its often down when its supposed to be up.
Video of my problem in action here:
Thanks for any suggestions.