Sounds like your XB relay is firing when the Player Unit is in position 16 rather than position 17 as it probably should for a 2 player game:
Jumping Jack XB relay (resized).jpg
I would guess that either the P2A make/break switch on the Player Unit or the normally closed switch on the PB/2nd Player relay is closed when it should be open. If you don't find an obvious problem with either of these, you could take your game to player 1 ball 5, then put slips of folded paper between the P2A and PB switches and the third switch (not in red) on the P relay to see if that fixes the problem when you let the ball drain. If it does, repeat the experiment and unblock one of the blocked switches each time until the problem returns.

/Mark

Cool. If the jumper from the P1C switch is really wired to the white-green wire that effectively removes the P2A switch from the circuit. I think your solution is correct.