Yes you are correct, I flashed ArduPilot instead of PX4.
Any way, one observation that I made an hour ago where I went to AutoTune my quad was that on first attempt, it showed me the same issue of trying to flip!, I had my laptop with me so I calibrated level only!!! and the quad lifted like never before.
So, I believe the quad must be truly leveled before takeoff. I am now sure that this was my whole problem.
Since you use QGC, You can send it the level command from your phone or something?
Just to elaborate a little my understanding (I don't know much), any one please correct me if I'm wrong: since we fly initially in Stabilized mode it basically means that all signals to motors are sent by the FC based on what it "thinks" the state of the quad is in the X,Y,Z space and I think that the issue with the RCOut 3 low, is the same as mine was RCOut 3 flat line - so in my opinion your FC thinks that it doesn't need to raise the RPM on motor 3.
All the above is only if I figured it out correctly .