A little background. 

This flyaway occurred on a dji s900 setup with a Pixhawk fc, dji hardware, and an ImmersionRX Ezuhf diversity receiver. I've flown this setup countless times in loiter, auto, and stabilized flight modes without problem. My transmitter is a Taranis Plus with ImmersionRC EzUhf transmitter module. I always fly with missionPlanner open and connected on a ground station laptop and have had success with using that radio connection for flight mode changing / auto mission waypoint selection. 

Now for the flyaway. Here is a short video clip from partway through the flyaway. The Diversity monitor I was using at the time of the flight didn't have a DVR so the only dvr I have is when it was already out of sight and I grabbed my FPV goggles and started recording with its DVR. The craft was on an auto mission (~200 meters away) when it suddenly tipped forward and to the right and then started acting very weird (while in auto ie shouldnt have been happening). I immediately switched to loiter which gave limmited control and I tried to bring it back to me. It still wasn't responding correctly though and so I switched to stabilized mode which still yielded little to no control. The craft wasn't losing altitude, just not responding correctly to my commands. At this point it had come back and was only about 100 meters away from me at about 200 feet altitude. At this point I could see from its FPV feed, from a hard mounted FPV cam, that my attempts to yaw or roll the craft with my transmitter in all flight modes were not having any effect on it. At this point I switched to failsafe mode on my transmitter, but the craft continued to switch itself back and forth between loiter and stabilized mode rapidly. It passed me at this point in the opposite direction of its auto mission and then seemed to get stuck in stabilized mode and started flying full throttle away at a 24 degree heading (Ive had the transmitter in RTH mode for a while now). It ended up flying full throttle for about 12 minutes before coming down about 3 miles away. I have looked at the logs in mission planner etc and can't figure out what exactly happened. Any advice or insight would be great!

I had to compress the bin file since it was 8.7mb, so the bin file is and kmz files are attached for reference. 

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Posting to discuss.ardupilot.org will probably be better for you

From your log, there is a very weird CTUN Desired Altitude that becomes negative to -100 meters erratically on long periods, then comes back to same values as the effective altitude for a short while then dips back to high negative values.

A baro issue ?

Also there is to be by moments very high vibrations, that stop by moments, then again high vibrations. that makes me think about something touching/bumping your flight controller by moments : a loose cable ?

High vibrations are known to be a cause for flyaways.

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