I’m getting a very odd behaviour in my Skywalker’s (with Pixhawk and APM:Plane 3.3.0) RUDDER . While in Manual Mode it responds correctly to the transmitter’s input, in other modes managed by APM (Stabilize, FBWA, etc.) not only does it move in the wrong direction but it also bounces along the movement. The video explains this oddity better than words: drive.google.com/file/d/0B9G60c … sp=sharing
Looking at the video it looks like you have either V-tail or some other mixer active.
In FBWA quickly yaw the airplane nose right and the rudder should go to the left trying to stop the yaw rate. If it goes the wrong direction reverse the rudder in the Mission Planner.