All output ch of Pixhack not working after flashing Arduplane 3.9.5 (ChiBios)

The Rx feeds control signals via a PPM encoder to the RC in of Pixhack 2.8.4., which is flashed with Arduplane 3.9.5. During flashing, I was asked ChiBios, I clicked “Yes”. But all the 4 basic channels do not work. ESC calibration and arming by rudder ch are also not possible.

I found in Wiki, it says " Recent versions of ArduPilot (Copter-3.6, Plane-3.9, Rover-3.5) run on relatively small, non-Pixhawk, flight controllers using the ChibiOS operating system. Examples of these boards include the OpenPilot RevoMini…"

Does it disable the output if I flash Plane 3.9.5 to Pixhack/Pixhawk ?

The flight mode channel works fine for all the 6 modes.
Thanks for your help.

Further to my last (initial) posting, I re-flashed Arduplane 3.9.5 to Pixhack NOT using ChiBios, but with same result… all 4 basic channels do not work. I by-pass the encoder and connected the servo directly to the Rx and the servo works. I even used different set of Rx and encoder, but did not change the result. Flight mode still working without problem. I measured the voltage on the output rail of Pixhack with CH 3 (BEC) connected, and it is normal at 5.3V.

The only difference after I flashed not using ChiBios, is I got both Ch1-4 input AND ouptut PWM (except Ch 3 output, b’cos I can’t arm the motor) in the Status tab of MP.
Before when I flashed using ChiBios, I only got Ch1-4 INPUT (incl Ch 3) only.

Does anyone have any clue.on what’s gone wrong ?