So heres the scoop. I had a well flying quadcopter using an APM 2.6. I decided to move to pixhawk. Bought a brand new unit from 3dr. Wired everything up and installed 3.2 Took it out to fly today and wasn't able to get it off the ground. The throttle and motors seemed to be acting weird and it sounded almost like a grinding sound. Keep in mind these motors flew through two batteries just the other day on my APM 15min flights each without a hiccup. The only thing thats changed since then is the flight controller. I brought it home and flipped the props and went to work trying to debug. I did the motor test in mission planner and ran each motor up to 15% throttle. Everything seemed fine, no weird grinding. So I got my camera out and started recording while I armed and tried the throttle. Again I was getting the grinding noise, then I noticed that above 50% throttle it seemed like no more actual throttle was being applied but the grinding noise got louder. I blipped the throttle a few times and sure enough it would seem thrust was coming up to the 50% point and then it was just making a louder grinding noise but not giving anymore thrust beyond that. SUDDENLY all the motors went to full power. No grinding noise anymore. I closed the throttle but nothing happened it was stuck wide open. I tried to disarm but it wasn't responding, so i took cover behind the bed as you can see in the video. The whole time I am trying to disarm. Eventually unsure of what my best move was I decided to turn off my transmitter. A moment later the motors returned to idle and I was able to disarm through my laptop (which I might have been able to do all along but in the rush I didnt think of it).
To put it lightly, what the hell is going on.
Video here, you can hear the grinding initially (warning loud)
Photo of the carnage below.