Onboard mag calibration doesn't complete on ArduPlane 3.9.0 up to 3.9.1beta2

When I try to calibrate compass using both NuttX and ChibiOS versions of ArduPlane 3.9.x firmware it doesn’t complete.
It reaches up to 99% but MissionPlanner never tells you it has succeeded and you should reboot.
Actually if you reboot you can find that it was calibrated; i.e. new offsets set.

I’m using Pixhawk1. I’ve tried the 3.9.1beta2 version too, no success.
It’s working fine on 3.8.5.

I’m using latest MissionPlanner 1.3.58

Not sure if it’s ardupilot or missionplanner issue.