When you say you are getting a 2 ball multiball when the gate opens do you see the Magneto animation that signals a "real" multiball has started?
I would check your switches/opto's on the main ball trough (Next to the shooter rod). On occasion mine will spit out an second ball and in a sense gives me a two ball multiball (No animation, just 2 balls on the playing field). When you accidentally end up with 2 balls on the playing field XMen pro doesn't end the turn once the first ball drains and allows you to continue playing until the other ball drains aswell. It seems to me that your game thinks its missing a ball in the main trough and is trying to get back to equilibrium by continuing to spit out the ball in the Magneto lock.