I know this is an old post but I was having the same problem, found this thread via a search and thought I would let folks what fixed it for me. I admit I'm pretty much a newb so I apologize if this is old info for most.
For me I was changing some lights over to LED and after doing so I started experiencing the same multi-ball issue. It turned out that one of the micro-switches in the subway was hitting a wire that I must have bumped. When it was got in contact with that wire it prevented the microswitch from closing once it got opened. That caused the issue. Once I moved the wire out of the way and the switch worked again the multi-ball problem was resolved. I hope your solution is as easy as that.
Steve
Manteca, CA
