I have kind of the same situation on my WhoDunnit. When the ball gets into the left ball lock saucer, it has a delayed recognize period, or goes all the way to ball search before recognizing it. If I hit both flippers and nudge the cab at the same time twice, it will recognize the ball. I've checked the switch in test mode too with fine results...but I didn't use the ball.
No cold solder, no loose joints, testing appeared fine. I will be very interested to see how yours is resolved even if it isn't the same system. The switches are probably still the same.