Hi, I'm looking at your log. It looks like your plane was never in Auto mode... MODE.ModeNum never goes to 10. (which I believe is AUTO?, that info is in defines.h) It seems the plane was in Stabilize mode (Mode 2) when it armed, and then FBWA (Mode 5) for what seems to be takeoff, then Stabilize mode (Mode 2) for ~70sec while climbing in altitude. (I think this was your first post-takeoff "flight" portion)
At ~200 sec in the log, something goes odd... I haven't looked at all of it. But at 208 sec, a Throttle Failsafe causes the plane to first circle (Mode=1), then RTL (Mode=11). Beyond this, I see Mode 8 (AutoTune), Mode 2 (Stabilize), Mode 5 (FBWA), and Mode 0 (Manual) at several portions in the log. Manual is the final mode, I'm guessing you used this to bring it home and land.
This seems to contradict what you said happened in your post. (Putting repeatedly into AUTO and FBWA) Did you perhaps upload the wrong logfile?