I would start by testing the switches in the ball through with a ball itself not your finger. Cause MB starts and 3 balls should be on the playfield and 3 should be in the through. One of the switches in the through may be registering as open during MB so it thinks there's 3 or more balls on the playfield already.
Also does it do this when you get Royal Rumble muiltiball when it fires all 6 balls?