Apm to pixhawk nightmare

Well been using apm for years all good.
Decided to go to pix hawk for a refresh.
And it flyers well in stable mode.
Now loiter…
The pixhawk comes back with compass varience. And tried and tried but not working.
Even in plugged the l2c port so it had to use the internal one which seemed to work but would “drain plug” as the compass was out a little on the pixhawk.
When I Connent the external compass again it is always out and I cannot figure out why? On a wooden bench in the garden nothing metal around me. Any ideas

Ok, what firmware are you using? Did you do the dance and get good numbers back? Did you check use both compasses or just one?

Can you tell us what the numbers are?

Mike