Menno,
Really not sure. The only thing that I can think of that we fixed the length of the compass vector on the pixhawk. It was too small previously because we were applying it twice. Hard to imagine how that change could affect the compass calibration though.
All the compass calibration code is done in the mission planner though so I would start by checking the mission planner’s status screen and make sure that the mag x,y and z values are being send via mavlink.
-Randy
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