Auto tune crash help - logs attached

I’m working on building a 650mm quad with a Pixhawk. Using 12 inch props with 650kv motors with 4s, Pixhawk, Arducopter 3.1 stable. It flies well in stabilize and altitude hold. On the first try, auto tune got through several roll twitches before what looked like one corner dropped and it fell. Second try, invoked autotune and it just came straight down, again, looking like 1 or 2 motors on the same side stopped. All motors and ESCs work fine when connected direct to a radio, and ESCs have been calibrated. Any input would be appreciated. I read about an ESC sync issue but cannot replicate this with manual throttle inputs, so not sure if that is the issue.

Today I was able to reproduce the problem during static testing and it seems like a faulty motor or ESC. Rapid throttle transients will cause the ESC to lose sync with the motor and the motor will cog or stall totally.

This is strange because all of these parts came off of my old quad which used an APM 2.6. Is there a difference in the output signals between APM and Pixhawk?