Copter pauses during Auto flight

We have several DJI S900's using Pixhawks, and in the past couple of months, we've noticed the copter "pausing", or at least wide swings in speed from the planned speed. This seems coupled with the inability to hold the planned altitude very well.  Anyone else seen this, or know why this might be occurring? I'm attaching a sample log. Vibration levels seem reasonable. This flight breached the altitude fence (10m higher than mission alt) and also tipped over on landing doing a good bit of damage.

2017-01-27 14-06-21.bin

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  • IMU Mismatch: FAIL Check vibration or accelerometer calibration. (Mismatch: 3.29, WARN: 0.75, FAIL: 1.50) 
    Motor Balance: FAIL Motor channel averages = [1532, 1544, 1520, 1559, 1539, 1537, 1734] [GRAPH]
    Average motor output = 1566
    Difference between min and max motor averages = 214

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