I have an apm2.5 with a cheap Chinese neo-6 ublox + compass V 2.0 board
and have been having problems in auto mode and circle.
on investigation i found that the mission planer compass display was very non liner
compared to the actual heading several re calibrations were tried some better some worse
on looking at the board i noticed that there is rechargeable battery underneath the magnetometer chip
so i unsoldered this battery, re calibrated and all non linearity disappeared !! ( and low offsets)
placing the battery near the chip pulled the indication way off
lesson learned (again) Don't Bye Chinese Clones!!
So if you are having strange bhaveyer in auto modes and have this v2.0 board
throw it away and get a real one