Sounds like I may have a similar problem but not sure. Very strange things are afoot.
Something more seems to be happening more and more now on top of it unwantingly choosing a mission on a flipper press at random times, either at start of game or in mid-game.
It will suddenly add a ball as if it thinks the ball has drained. As well, sometimes it doesn't seem to register that the ball has drained and goes searching for it.
I noticed once while I was in a Vengeance Multiball mission that after all the balls drained, the mission didn't end and when I hit the flipper buttons, it kept adding to the score. Only if I held off for awhile would it go into ball search and it did that a few times before it finally ended the mission.
So, a bunch of wonky stuff going on, but I don't know enough to figure out where to begin looking for trouble. I'm hoping what I've described can help narrow down the possibilities somewhat.
It started off as the mission selecting thing a couple months ago and was slightly annoying, but now it has gotten exponentially worse and close to unplayable until fixed. If I can't figure it out, may need to get somebody over to help out.