It sounds like you are using INS13, not Basic (attitude estimation algorithm) so that you can use GPS flight modes. With that come several things you did not need to worry about with Basic (CF).
For the current release it is important that:
- you don't use tilt motors
- your FC and GPS/mag are mounted level
- your FC and mag are pointing in the correct direction, either the arrows must point forward, or you must adjust FC "Attitude - Rotate Virtual" and mag "rotation" and those are somewhat confusing and take time to learn and understand. It is thus much easier to just make the arrows on both boards point forward.
- You calibrate the mags carefully via telemetry, outdoors, away from metal and ground the whole time you are calibrating (not just each time you press the button.
- You test outdoors because GPS jumps around more indoors.
If you don't do these things, then when the GPS gets enough satellites and Stab and Atti go green, it can go crazy in the PFD/HUD/AH.
Some of these rules can be bent a little, but follow them closely till you get success that you can fall back on if problems arise.