A while ago I set up flaps on my Bixler with my Turnigy 9x. That worked well for a while but they didn't work too well in stabilize (APM2) (servos would go wrong direction) so I got rid of them. Or so I thought... Now I have no flaps switch, have reset the firmware and my plane worked well for a while.

Oddly, today I was flying and when I engaged Fly by wire mode (it was only fly by wire mode) the plane put the elevator down and ailerons opposite directions causing it to crash. No other switches were switched and up until now the plane had worked fine and no other modifications made to the plane between when it was working and now. To clarify, after I got rid of the flaps the plane worked well in all modes. What could be causing this?

Additionally, when I switched to manual in order to prevent a crash the plane was stuck in the crashing mode and the effects were worsened. What could have happened? Is the APM faulty? Is this a software or a hardware issue?