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I'm wondering if anyone might have any suggestions here. 

I'm trying to compile Arducopter and running into a strange issue - I've followed the instructions, set up GitHub, the PX4 toolchain, I clone the source locally, update submodules and it seemingly compiles fine.  I get a .px4 file which flashes in Mission Planner without issue.  But that's where things start to go off the rails.

When I compile the latest source and flash the firmware, when I connect to the flight controller, the entire RATE section in the parameter list is missing and all the text boxes in the entire PID screen in Mission Planner are grayed out.

Ok, so I roll back to a previous release - 3.3.3 rc1, rc2, etc, compile and flash.  The PIDs are back and I can set everything up and the quad flies fine with the exception of all GPS flight modes fail to work.  My logs are full of err: FLIGHT_MODE-17, err: EKF_CHECK-2, etc, and the status light starts flashing yellow/red/yellow/red.  It still flies fine, no glitching whatsoever, it just won't engage any flight mode that uses GPS.

When I flash someone else's compiled firmware, or one from Mission Planner, everything works perfectly - Rate parameters are there, GPS flight modes work fine, no errors to be found. 

What am I doing wrong?  I'm compiling on Windows using the instructions "Building for Pixhawk/PX4 on Windows with Make".

The reason I'm trying to compile myself is to make a small change to the AP_Compass_PX4.cpp file to set all compasses as external.  I'm using an Airbot PX4MiniAIO, which doesn't have an onboard mag, so all compasses are external, but the firmware seems to always set the first one as internal on reboot.  I can change the parameter and it flies fine until the next reboot, when the compass gets set back to internal.  I need to set the orientation to Yaw180, which is only read if the compass is external. My change successfully sets all compasses as external, but the GPS flight modes stop working.  I lean towards these not being related, because when I compile the source without my change, I get the same thing - GPS modes don't work.

The GPS/compass is pretty close to the other components, and that might not help, but I don't think it's the issue either since it works fine on firmwares other than those I compiled myself.  This is the quad I'm working on:  170mm PX4 Quad 

I wanted to see how small a quad I could build that would include a full autonomous capable flight controller, GPS and the works.  Everything is working great with the exception of the compass getting set to internal.  I'm better at hardware development than software! ;)

Thanks for any help anyone can give.