Yes I think GPS is great, but we may rely on it too exclusively. I may allocate one of my six APM modes to MANUAL in response to this, and other reports I've seen in YouTube videos and on forums. It would be interesting to know what logical sequences the controller boards use to make flight decisions, and how such decisions are made in the event of conflicting indications from gyro compass and GPS. One of the three is probably being given more weight than the other two, and I'd guess it's GPS!
I wonder if the telemetry on an APM controller that returns to base and gets recorded includes streaming readings from all the sensors (or if it could be made to)? That's probably a question for the DIYdrone forum mainly supporting ArduPilot (3DR). I have a "knock-off" of that board -- the ArduFlyer. At different times, they were made in the same factory from the same components and on the same line! But of course, that's a sore subject over there.
Now they claim theirs is made in Mexico (like that's BETTER), and they use tighter quality controls, yada, yada, yada... Not from reading the reports of failures they don't! And if you want a monopoly on your product, don't start with OPEN SOURCE! DUH! But you can't reason someone out of something they weren't reasoned into, so I let it be and get the help and info I can.
I think Dennis Baldwin also just posted a YouTube video on using APM logs to diagnose failures. In it he claims to have poured through the log data for tens of hours, so he would surely know if granular gyro and compass readings were included in any useful regularity. I could just pull some ground data from my APM-based quad and then look at it, or even introduce movement. In ground tests, I've seen what happens when a GPS loses too many satellites.
I suspect the GPS lock state does not consider the reliability of satellites when deciding if a good lock has been achieved. Satellites on the horizons are used, when I think a lock on them is less secure and continuous than those at a steeper angle. I read that it is important to have the GPS antenna above everything else, including the plane described by spinning carbon fiber props, as they are opaque to radio transmission and can impede a lock on horizon satellites. This may also explain why FPV antennas work better hanging below the craft than mounted above. Any multi-rotor that pitches or rolls is going to disturb the GPS' satellite vectors to horizon satellites, so I don't know what the answer is there. You can't put the GPS a FOOT above the drone in practical terms, and even if you did, a 20 degree roll with the motor on a fairly long arm will still shadow the GPS from low angle satellites at times.
But I ramble!
Good luck finding the solution, or just avoiding the problem by training that "assistant" to fly.