I did two flights today. One manual flight in stabilize mode, going into a loiter, back to stabilize, to RTL,and then landing in stabilize. Everything behaving as expected.
Then a second flight, with some waypoints set. Starting in stabilize, switching to auto. The copter moves towards the first waypoint. It gets high enough for me to get nervous (I had the waypoint at 200m - way too high, in retrospect), so I switch to RTL. It keeps climbing and goes in another direction. I go back and forth between stabilize, trying to get orientation on the copter, and dropping the throttle to get it down, and RTL, to hope it comes back, which it doesn't. I set it down behind a tree, with light damage: lost a prop, and one motor torn off the mount.
This is with 2.7.3 software. Any insights into the RTL behaviour would be very helpful. The copter orientation seems to jump around abruptly when I look at the log file in APM Log Visualizer 1.3.
(Edit: this an APM2.5, with the internal mag. My APM2 with external mag is in another system.)