Unable to Calibrate Compass with EKF2 enabled

Not sure where to post this so just let me know if there is a better thread elsewhere. Using Copter 3.6dev with UAVCAN compass and GPS module. I can see the data coming in on the status screen of Mission Planner so I know that the compass is working but the Mission Planner compass calibration does not even see the external UAVCAN compass or the internal either. This is Arducopter v3 on a Solo. So I had two Pixhawk cubes and found one worked and one did not. I diff’ed the parameter files for each and found that the one that did not work had EKF2 enabled and the one that calibrated fine had EKF2=0. One of the versions of 3.5 that I was testing must have changed the default to EKF2 enabled because I did not set it myself and when I loaded 3.6dev it did not reset the parameters.

I read that EKF2 is now default enabled since some version of 3.5.x but with it enabled I can not use Mission Planner to calibrate the mag. If I turn it off the mag cal works normally.