One thing you might try is to adjust the opto boards positioning ever so slightly. I had a game where it definitely seemed like the opto boards were aligned as you could see the red light shining through to the receiving board with a red halo, but in fact it didn't register consistently. I used the service menu clear ball mode to see on the DMD when it registered where it thought the balls were and it helped out. It's now working great.

I thought I needed new opto boards, or at least a new receiving board, but a good reflow of both of them for good measure and an alignment adjustment was all that was needed.

Also, I found I needed to disassemble and clean the ball trough coil mechanism (the one that releases balls into the VUK) and add a bit of oil to the moving parts so that it would function smoothly/consistently.

Hope this might help.