The first source of the overloading of either the boards in the controller for the autopilot or the fluxgate compass to concern one's self is obviously the power wiring. (Hot and nuetral.)

However, it's possible that he EMF or other emmisions might be overloading the circuits or being "recieved" sympathetically from your autopilot.

I think that the challenges of circuit boards that operate on relatively low voltage and amperage situations inherently offer an opportunity to clash with an antenna which emitting relatively large amounts of power.

If it continues to be possible, if the problem isn't from the power wiring, to protect the device with a Faraday Cage you might fabricate; however, why don't you see what happens first, then go from there. It MAY not be a problem, Max -- especially if you're living lucky these days :^)))