The work around is to start the mag calibration, go to the System tab, go to AuxMagSettings, and press the Save (red up arrow) button at the top of the page. I am a little unsure if it should be this Save button, or the one on the calibration page (which may be inactive). Also, it may be that you need to change some data to get the Save button to save?
I wonder if this would work too: Before doing calibration, reset aux mag calibrations to defaults by going to System -> AuxMagSettings. Set AudMagSettings.mag_bias to 0,0,0 and mag_transform to 1,0,0,0,1,0,0,0,1
then just do mag calibration normally.