It's not a software problem. I suspect that there may be a switch issue. So I suggest that you run the switch diagnostics and pay particular attention to the playfield entry and the two saucer switches. (But test them all.)

Based on your email it looks like the saucers work as expected in single ball play. Can you confirm this? Specifically, do they activate the bagatelle and release their balls afterwards without delay? Does the double-kick arrow work as well?

Finally, when you are in MB with one ball locked and you lock the second ball in the second saucer, does the bagatelle activate at all?

I am assuming that you have confirmed that the playfield entry switch works correctly when you roll a ball quickly across it? Because it is from this switch code that the routine is called that ejects the locked ball. However, the ball will only be ejected if the right trough switch is open. Have you confirmed that the trough switches work correctly? You'll have to remove the balls to test this properly. If the trough switch is stuck close, I think that the trough-eject solenoid (instead of the lock-eject) will fire when the second ball enters the playfield but I have not tested this.