Not intimately familiar with the lock mechanism on Rollergames but I would check the switch that detects that the second ball is locked. Since the game is working otherwise, I would rule out the trough. Perhaps the 2nd locked ball is initially detected when it enters but later loses contact with the switch. When you drain ball 3, the game doesn't know where ball 2 is anymore so it assumes it's out on the playfield somewhere and doesn't go to the end of ball sequence.

My BK2K would do this on occasion with a flaky switch on the 2nd ball lock.