I recently setup a ~400mm quad with a Pixhawk and 3DR external compass/GPS. Using all default values the quad flies pretty well, but I wanted to test out AutoTune to see how well it works. I noticed the AutoTune settings make the quad feel very twitchy, and unstable. When I went to land the quad immediately flipped over and despite throttle at full down, the motors continued to spin upside down, breaking props.
I thought possibly the AutoTune procedure didn't work properly, so I installed new props, restored PID values to default and tried again. After disarming and saving the new tune, and trying a flight with the new tune, again the quad flipped over in the same manner as before on landing, and again despite throttle down, the motors continued to spin.
I'm not sure what's causing this behavior, but I'm uploading the logs in hopes someone here has seen this problem before and knows how to resolve it. Please let me know if any additional information would be helpful.