Pixhawk goes out of control on a Research quadcopter

Hello there,

We built a quadcopter for research and development purposes. We turned on all failsafe parameters and checked all sensors calibrated correctly quadcopter was on a flat level and gps was working fine. First problem was when we started motors, there was an imbalance and when the throttle was at %40 third motor was stopped. Then I checked pwm outputs with an oscilloscope and confirmed the different pulses at stabilize mode. Later on we decided to fly with a telemetry module to see the problem still consists. We set the mode Loiter and altitude 2.5m. Led on pixhawk was green(3D lock 11 sat) and we pressed take off. Quadcopter took off to 3m and went outside the field without any user input and crashed. When we checked the logs GPS was no good and motor balance was bad. Should I understand that flight controller is broken or is it from the software? Appreciate for any help.

Best regards 

Quadcopter Setup:

pixhawk with arducopter 3.5.7

 T-motor U3 

T-motor air 40A ESC

Ublox neo m8n

Ground Control:

Qgroundcontrol on Ubuntu 16.04

 433MHz telemetry module

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