Pixhawk Looses Thrust After A Few Minutes of Flight

Hello everyone! I have been experiencing some issues with my custom built tri-copter running on a genuine 3DR Pixhawk purchased from their site. It will take off of the ground and appears to have a decent amount of thrust, but within 2 or so minutes of flying, the copter looses thrust. I will be giving it full throttle yet it will be slowly and  steadily moving downward towards the ground and then wont have enough thrust to lift back off after only a few minutes of flying. I am running a new 3S battery 4200mAh 50C lipo and after that 2 min flight the battery still has a charge of 85%. The battery does not seem to be an issue since I put it into my brothers quad copter and it flew for a good 15 min and I have tried other Turnigy batteries with the same issue occurring. I find it odd how it has plenty enough thrust to lift it off the ground in the beginning of my flight so I don't think it is an issue of it being under powered. I have played around with the throttle max, mid, and min parameters as well as the linear throttle curve parameter turning it on and off but the problem still occurs. Is it possible that the pixhawk is faulty? I attached the logs from my last flight if anyone can help me diagnose what is going on here, I would greatly appreciate it. The hardware on my tri-copter is as follows and I am running Arducopter V3.2.1 Tri:

3DR Pixhawk with the Power Module

3DR 20 amp ESC's

3DR GPS

3DR PPM Encoder

3DR 915 MHz Telemetry Set

Frsky V8FR-2 8 Channel Receiver

Emax Grand Turbo GT2215/12 Motors

APC 10 X4.7 SF Composite Blades

Emax 19g ES354 Metal Gear Servo for the tail

Turnigy 9XR is the Remote Controller

Here is a pic of the throttle out and in from the CTUN from the log of my last flight. I have attached the  log from the SD card of the Pixhawk as well.

3691234825?profile=originalI appreciate all feedback, questions, and insights. Thanks!

Thrust Loss from SD Card.BIN

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