I would add that it helps to have telemetry for this and it is nice to watch the GPS trail when doing waypoint flight.
Also, I assume you are running LibrePilot v15.09
Mag is a hard thing to get right via USB and changes when the USB plug is close or not. One guess has it that your mag is no longer green with USB unplugged. I would suggest that you recalibrate your mag:
- keep it away from all metal and computers and house wiring as much as possible while calibrating. No washing machines, no water heaters, no cars, computers as far away as possible.
- I've done it with a 3m/10ft USB cable and a remote mouse, but it's not optimal and shhhh don't tell anyone
- be aware that the calibration is recording all the time, so do not think that you can set it down on a metal cabinet between saves.
- before starting calibration, hold it up, away from stuff, click, rotate, click, rotate, etc. keep it about in the same place in space.
Minis and high powered quads are notorious for GPS mode problems when using the onboard mag. A high powered mini may not be possible with onboard mag. But you haven't got that far yet. Those problems only happen when the motors are under high current flight loading and the too close wiring of a mini messes up the on board mag. Do you have all your high current (battery to PDB, PDB to ESC, ESC to motor) cables twisted properly? That won't keep you from arming, but it will cause
bad problems if you try to fly it in any GPS mode.