PixRacer with Here-3 GPS

We are using a PixRacer with a Here-3 GPS. We have been successful with the Here-2, but the Here-3 has generated some strange issues. Today, I wish to understand how the Compass offsets for the second Magnetometer (in the Here -3) are defined/or obtained. According to all I have been told, the system learns the offsets during the accelerometer setup step, so why are Compass offsets defined in the Compass calibration check. Does anyone understand this issue? Thanks, Jim.