I haven't ever had anyone report any issue like this before, so I don't have a good answer for why the game is not wanting to operate each flipper independently. Since you have been able to confirm the correct operation in test mode, it certainly does point to it being a software issue, but it would be rather strange for the game to have been programmed that way.

As for the autofire coil interference, try flipping the magnet over (don't rotate it on the steel, but slide it off the metal actuator and then flip the magnet over (front side to back side) and put it back onto the actuator). Usually this will take care of the problem.

And as Jalpert said, please be sure to tape down the magnet after you are done adjusting it. Thin scotch tape is best, but anything thin sturdy tape should work. Just be sure to wrap the tape around the metal actuator so it has something to hold on to.

Hope that helps!

Tony