yeah, the expected behavior is after locking ball two, a ball should come out of the trough and fire automatically from the launcher.
the game obviously knows lock two was activated ... but then it doesn't eject a ball from the trough. hmm.
i assume your second locked ball is always at the drop target under the borg ship. have you tried locking the second ball by going up the delta ramp and into the back of the borg ship, or at the neutral zone? lock behavior from these other lock locations might give us a clue.
unfortunately, the game seems to turn those locks on only if the multiball percentage drops below a certain level, so you may have to reset audits or something. i don't think there's a direct setting to enable them.