Doesn't sound right to me. Although I believe there is a couple ways of getting a 2 ball multi-ball. Maybe that is what you are getting?

Check the 2 switches in the left lane where the ball locks, one may be stuck on, I had one that was not working once and had to stack two balls on top of each other in the left lane to count the balls.

Did you figure this out? I would guess yes but a possible reason that I will suggest for others with this problem. I would check your left ramp switch...if this does not activate the diverter lets the ball through and you get multiball.

Actually the left ramp should never start multiball unless the ball slips past the diverter (which is quite rare unless the switch on the left ramp goes out or becomes intermitantly registering). Multiball should start with the rocket (yellow ramp, or the right ramp only under normal operation)