Rotate onboard compass in software to match board rotation

Hello Forum,
I have recently put my quadcopter on a new frame and i had to mount my APM 2.5 Board sideways.
The Problem is, that even with changing the compass configuration to the right rotation and telling the Firmware that the compass is external (which it isnt), MissionPlanner still shows the wrong orientation.
It this a known bug? Is there a way to fix this except digging into the firmware itself?
Thanks in advance