Im no expert, ive just begun using a Pixhawk 2.1, but i saw something interesting so i figured id comment. You say your using copter 3.4.6? As i understand it only 3.5 beta will work properly on copter? I had a pixhawk 2.1 with 3.4.6 on it inadvertantly and it caused a ton of issues. It still booted and acted somewhat normal, but still there were alot of gremlins completely solved by having the proper supported firmware for the new controller.
This may not be your issue at all, but if you are indeed on 3.4.6 id flash 3.5 provided you are using a new Pixhawk 2.1