Honestly I would just call stern and have them provide some suggestions. I've had the aux board problem, but this doesn't sound like an aux board issue. I agree it does seem more mechanical, but the 1800KICKERS guys will sort it out for you.
Quoted from ChrisBardon:I've also noticed that the NC switches seem to be overly sensitive, since they score when dropped (new games for p1 start with 1110 points), or pop up then immediately drop in Rogue mode.
Yeah, nightcrawler slams so hard back into the mech that it scores, sometimes also scoring the Magneto lock targets. Something to bring up to Stern, they may have a suggestion on how to adjust the switch.
-Wes