Hello all, I just ran into the same problem with the latest stable PX4 firmware and the standard AETR airframe (my model is a Volantex Ranger EX).
I first built the plane without a FC at all, directly connecting the receiver outputs to the servos (Y cable for ailerons) and pusher motor, and did a flight test. I had to reverse ailerons, rudder, and throttle on the radio to get correct manual control of the plane.
Next I added the Pixhawk with PX4/Standard AETR and got it working in Manual mode. I left the radio channels as-is but the radio calibration seemed to detect and account for the reversals correctly. The only weird thing was that arming was lower-left rather than lower right, due to the rudder reversal. So I reversed the RC input channel and the PWM output for the rudder and arming and control all worked as I expected. Ailerons worked correctly in PX4 manual mode without further trouble.
So silly me, I next thought to test stabilized mode but forgot to verify aileron stabilization controls were in the correct direction. I had the same result as @Deafro. I had a spectacular flip and nose dive on my first takeoff. Luckily all damage was repairable and I'm ready to try again.
I tried reversing or not reversing the aileron RC input (RC1_REV) and the PWM output (PWM_MAIN_REV1) in PX4's settings but as @Deafro found, it didn't seem to make any difference. No matter what I do, roll correction is always backwards in stabilized mode. Gyros are detecting roll correctly and the target roll speed is always in the right direction, but the ailerons always move in the opposite of the correct stabilization direction.
Does this mean I should go back to the beginning with un-reversed radio channels and a fresh radio calibration, get the controls working in manual, then try again to get correct control in stabilized mode? Do I need to mess with PWM_AUX_REV1? I am using the main outputs per the documentation, not the aux outputs, so I don't understand why PWM_AUX_REV1 would be relevant.
I will go ahead and try all of these possible solutions, but I feel I am either misunderstanding something or doing something unexpected by leaving channel 4 reversed in the radio then setting RC1_REV and PWM_MAIN_REV1 to correct for it. As others may have the same confusion, I thought I'd ask here.
By the way, great community; I've been using PX4 for multicopters for a while and love it! Thanks for helping a newbie on planes.
EDIT: Got it sorted by resetting the radio to normal for all channels, turning off all RC and PWM reversals in the PX4 params, then experimenting. To get correct behavior in manual mode I would first reverse the PWM main output if backwards, then if still backwards in stabilized mode, I would reverse the channel on the radio and recalibrate the radio. Will try a test flight today. I am not yet convinced that flipping RCX_REV has exactly the same effect as reversing on the radio.
Is this a bug, that stabilization controls can be different from manual controls? I would think that both the manual controls and stabilization controls should be in the same direction depending on the radio calibration.
Also, I don't think this is documented for planes. I'd be happy to contribute to the docs.