Compass Calibration renders compass useless

#### Issue details
I've already described my issue here: https://discuss.ardupilot.org/t/all-magnetometers-0/36131/3
I have an issue with the compass calibration (only checked it with the internal one).
The compass calibration works and it says successful, but as soon as I reboot the Pixhawk, all magneto values are zero. The only solution I've come up with so far, is to reset all values to default, than the compass works again (but isn't calibrated).
Today I've also tried it with QGroundControl and it worked flawlessly, so I'm assuming this is an issue related to mission planner.

#### Version
1.3.62

#### Platform
[ ] All
[ ] AntennaTracker
[ x ] Copter
[ ] Plane
[ ] Rover
[ ] Sub

#### Airframe type
just the bare pixhawk for testing

#### Hardware type
Pixhawk

Start by reproducing compass calibration in Mission Planner 1.3.62 with the bare Pixhawk setup described, then reboot and check whether the magnetometer values become zero. Compare the result with the reported successful QGroundControl calibration and verify that a completed Mission Planner calibration persists and leaves usable compass readings after reboot.

Written by the indexing model from the issue text.