I believe my game may have had the same problem as you're describing:
Balls 1 & 2 would lock as they should when Lock was selected on the skill shot.
But despite not obviously being offered the Lock selection for Ball 3, Multiball would start after Ball 3 was launched no matter what was chosen.
The problem on my game was simply that the micro switch blade was out of adjustment on the drop target. Try adjusting it or replacing the switch. If you replace it, you might either have to cut down the new blade or you might still end up transferring the old blade--so regardless, watch out for the adjustment.