First off, all ideas are greatly appreciated. I am flying a stock Bixler with a mega 2560. it does have an airspeed setup. The plane has flown 5 times very successfully with manual control. I am using a TX6A Futaba with channel 5 set for mode selection. It is a 2 position switch so it is manual/auto only. I have gone through the complete radio and autopilot setup. I am assigning waypoints from mission planner with the GPS locking on home very reliably. When I switch to auto, it continues straight and is stabilized with my only control being rudder. It doesn't even try to go to a waypoint. I have flown in perfectly calm conditions. No telemetry yet so I load the waypoints, shut every thing down, go outside, power up, and fly. When I select auto on the ground the controls conteract pitch and roll changes as it should. I have got to be missing something here............Thanks all!
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Whats' your waypoint radius set too, and how far apart are your waypoints? if the circumference of the waypoint acceptance is really big, it will just accept it made it and move on.
Also to test if your plane will fly auto, try flying FBW-A and FBW-B first as this will confirm your have your parameters set up properly.
If you have telemetry logs (flogs) or data-flash logs posted it's much easier to determine these questions
Thanks