Glad to hear I'm not the only one that is seeing issues with the trough. I was 100% certain it was code related, as I didn't have any issues like that just minutes before the last code update.
No matter how good the new code is, the truth is I can't play the game this way, it's 100% ruined just as Cheeks has said. So often the ball thinks its dead and the flippers go dead, when there's no reason for it. Then other times the ball gets stuck in the trough, and shaking it wildly seems to get it unstuck, but by then you've ruined the flow, and likely tilted 
Thanks Charlie for looking into this, as none of my pinball friends want to play it until it's fixed, and being impatient, I put it up for sale. 
-S
Quoted from Cheeks:This has become a huge issue for me as well. I have it WAY more often than 1 in 10 games. I would say at least one ball to the plunger per game. I've had this totally screw me out of a multiball countless times because the game thinks it served the ball, but they're just stacked in the plunger. This used to be a minor issue and has certainly gotten worse recently.
Pipe Creek, TX
