I've installed a Pixracer flight controller into a Reptile S800 with the latest ArduPlane firmware (3.9.8; installed in Mission Planner automatically) and configured it up. Everything works properly, all components are operational, the plane is armable (with a full arming check) but the autopilot doesn't control the throttle and the elevons.
In manual flight modes (manual, stabilize) it works properly; the throttle and the elevons can be controlled by RC. In FBWA mode the throttle also works (as it is manual). In Auto flight mode the throttle work during a hand-launched auto take-off (the motor speeds up) but after that nothing happens.
No servo and no throttle control in any of the automated flight modes (FBWB, Loiter, RLT, Auto, etc.). No error messages.
What can be the problem? Is there a bug in the firmware?