Today I tried a test flight with pixhawk 2.1. When I switch to auto the aircraft throttle drops and the RTL mode goes on. The aircraft flies fine but with altitude keeps dropping while the plane holding attitude very well. Failsaif was disengaged.
When you switch to manual throttle comes back and you can fly the plane with full control.
In another test today i keep getting RTL while flying the mission. I had to toggle the switch to auto every time RTL notification flashes.
I am sure I am missing some autopilot configuration