"Simon Kirby responded to my youtube video with the following:

Hi, all! It turns out that the pixhawk (http://3drobotics.com/wp-content/uploads/2014/02/px4fmuv2.4.3_schem...) uses TXS0108 buffers on the motor PWM outputs. This is a bidirectional…"

"Ah, well since it works on the 5V BEC, even through the Pixhawk, I don't think that's the problem.  

Now I'm no electrical engineer, my day job is as a computer admin.  But my best guess, at least in my specific situation, is that it is a ground…"

"Artem, not sure what 3.3v would accomplish.  It already works fine if I 1. Disconnect the power module from the Pixhawk (or remove it entirely) or 2. Control the motor directly sans Pixhawk with the 5V BEC on the receiver. 

But sure, I can take the…"

"I can send mine back to you if you wish.  As per my latest youtube video the problem still exists."

"A long time ago, it doesn't fix the problem."

"Just the BEC on the Afro ESC."

"No, I didn't, but it happens both with my 2200kv motor on a 3S 2200mah lipo, as well as on my 1100kv motor on a 4S 3700mah lipo, so I doubt it is related to the battery."

"Here you go.Power Module.BINNo Power Module.BIN"

"The setup that was sent to Craig was mine, I don't know how you would describe the wiring on it a 'dogs breakfast'.  It is just one motor, one speed controller, and the power module.  When I sent my setup to Craig, he was exceedingly nice and…"

"Sorry, I've been through all of this and still I have to back up FlyHigh, there is something odd with the Pixhawk (even despite what 3DR is saying).  

If you watch this video, you can see that even with the ground wire connected it still has the…"

"I sent in the combo to Craig @3DR from this video: https://www.youtube.com/watch?v=u_KZ5K0R7eY&list=UUYZ_ZGYHxt_CX... He still has it.
 
He was not able to replicate my issue though, which was odd since I think the issue was pretty clear in the…"

"Thanks for the reply.  The receiver is set to go to the values it has when it first boots, so neutral sticks and throttle at 989.  I guess it is possible the receiver glitched for some reason and sent the 0 values, but shouldn't it have then…"

"I'm bumping this because I've yet to receive a response.  I've already purchased a new transmitter and FrSky receivers in the off chance it was my Assan hardware that was causing this.  I have done some bench testing but have not been able to…"