Thank you, that is a much more useful log for debugging. I will link to a firmware file and parameter file tomorrow, and we can see if you still have problems with that. I am using the BlueROV frame config and have never had this behavior. I would really like to figure out what it is. If you use the firmware and parameters that I am using and still have the same behavior then that will help narrow it down.
It is still intriguing to me that channel 5 is at zero instead of 1000 for stabilize mode. What are you using to input the pilot commands?
One thing to try in the meantime, in the default parameter group set and save GND_BASE_RESET to 1, then reboot the board, all while in the air.
You should also recalibrate your accelerometer and compass. Make sure that when you calibrate compass, the flight controller is in the enclosure with all other electronics, in the same environment as when it is flying. ie, put the whole rov together and spin it all around during calibration. Setting compass_use to disabled should mean the compass calibration doesn't make a difference, but I am just trying to cover all bases. Your calibration seems to be ok because the heading and attitude is solid when it isn't moving, but it doesn't hurt to recalibrate.