My guess would be the problem is that you are merging two lanes into one to close to the payout motor. That was my first design and had a similar problem. So, I merged the balls to one lane further down the line. I merged them together in the plastic piece that covers the back of the machine. So, in other words, the balls leave the payout motor, drop into the payout chute and at the bottom of the payout chute they enter into channel that leads to the front payout tray. I merge them together in the plastic channel, right before they come out into the payout tray. I also designed the "merging them over into one lane" similar to how the top tray is designed, with a curved built-up angled piece.

Again, without tearing the whole machine apart to show you, I made up another piece to help show how I designed the piece.002.jpg