Pixhawk sync issue on Align hexacopter M690L

Hey guys, first post here, but nice to join the community.
I’ve built up an Align M690L rig that’s powered by a Pixhawk. Using the stock Align motors and ESC’s, the Align PMU (power unit) to distribute power from battery to ESC’s. The Pixhawk provides the PWM signal that drives the ESC’s however. The drone is working well, tuned the gains with AutoTune, pretty crisp. However, when I started doing automated waypoint flights, it flipped, and crashed. (Happy to discuss what I had to do to get the Pixhawk to work with Align, mostly a list of random harnessing stuff). This is pretty reproducible behavior.

I’ve looked at a ton of telemetry, and my theory is that when it’s approaching the last waypoint, or when RTL is commanded, it causes a fairly sudden spike in the throttle command from the Pixhawk. This in turn causes a sync issue with the motors, and that is the source of the flip. This is just a working theory, I don’t have a whole lot to prove it, except when the hex landed after an almost unsuccessful RTL, one of the motors wasn’t spinning.

So my question is: has anyone seen and/or resolved sync issues with Pixhawk and Align ESC’s (aligntrexstore.com/Multicopt … 04001_p_….)?
On a broader scale, what are some ways that people resolve sync issues? Do you decrease/increase the RC_SPEED parameter? I’ve seen people also twist the ESC power cables. Any general tips to move forward?

Thanks for your support. Logs are attached, flip at the very end.

Motor sync issues usually have nothing to do with the controller but with ESC configuration. You might want to look into that first.