Unexplained crash on first flight


We were testing our large quadcopter with the Navio 2 for the first time today. It flew for a couple minutes, then one of the motors seems to have cut out. The quadcopter has flown successfully with a naze32 before this, so we are pretty sure it is something with the navio.

Navio2 with Raspberry Pi 3
Output from emlidtool info:

Vendor: Emlid Limited
Product: Navio 2
Issue: Emlid 2017-03-23 5e28de2c424cadfb61a62b88e9c0af98a6d25545
Kernel: 4.4.36-a7765e7-emlid-v7+

This is the Jessie image

I went through the radio calibration, accelerometer calibration and compass acceleration. However, the compass acceleration was done indoors, so it probably is not the best. Also, it was probably not very level when the accelerometer was calibrated.

Here is a video of the flight:

Here is the flight data:

I took a look at the data, and I can see that the motor that seems to have cut out (motor 2) drops in speed right before the end of the log.

Are any of you able to give any assistance?
Is there any other data I can provide?

Thank you

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