I posted on here a few days ago with a auto problem but didnt hear anything back. After installing the external compass I tested it will stab - loiter - RTL and it was ok.. Not great but ok. I then did a very short auto mission with a take off one wp and rtl to see if anything improved . Put it into auto and it flew out of here like it was a jet and started to pitch and roll all over the place I took it over to stabilize and got it back. I am posting the info here if someone could please take a peek. I would not doubt something is wrong with a setting possibly. The compass is on a small oh about 5 inch plastic stand off next to the apm 2.5+ ( running 3.0.1 and this is a 3dr hexa) Compass is hardware down with the arrow forward matching the apm in the setup I selected the external and its set at 180. I did notice it changed it to 180 in the manual box but nothing else stayed check marked I am assuming this is normal. But when you assume it usually ends up in the garbage can.
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I did want to add that I did run a Auto Mission which went off without a hitch so I am glad I put some time into diagnosing what was going on. I also think even though I don't have much vibration adding the high end rubber dampers under the apms mounting platform probably was the icing on the cake. Ok gonna close this one up guys.
There's still a reasonable amount of compass interference which is strange considering you're using an external compass. I guess you followed the instructions and cut the trace on the board so that the internal compass is really disabled? There's a video here.