After flying well for minutes, FBWA wants to crash the plane

Please see log at,FBWA.BIN

This plane is being tuned, please observe the strange FBWA behavior around line 39500.
This happened the day before in FBWB too.
Strangly, it flies very well in auto.

What’s going on ?

Not enough information. I don’t know what I’m looking for. When you say line 39500 that is this line:
2015-04-16 20:53:07.96: EKF2 {TimeMS : 1099601, Ratio : 48, AZ1bias : -2, AZ2bias : 0, VWN : 0.0, VWE : 0.0, MN : 225, ME : 30, MD : 570, MX : 0, MY : 0, MZ : 0}
and as far as I can tell at that time you were in Circle mode and didn’t enter FBWA until 20:59:22. Your flight was 1hr40min roughly of which you spent just over 2 minutes in FBWA.
What is the problem exactly?
Thanks, Grant

I did not mean that very line, but shortly after.
What happened is after a good fbwa flying, it starts to drive, until I take over in manual mode.

Can see a large drop in height at around 24minutes, but you were in AUTO mode at the time. You switched to FBWA to pull up.

Same again at around 45minutes, you were in AUTO mode at the time. You switched to FBWA and then Manual to pull up.

Same again at 65min, you were in AUTO and the plane loses height, you switch to MANUAL and pull up.

I can’t see anywhere where FBWA causes a nose dive.
Have you run AUTOTUNE mode yet? strongly recommended before you attempt flying in FBWA or AUTO mode.

Around line 398512 , I switch to auto.
Before that you can see a rapid drop from 100m to 64m, (RelAlt)
Airspeed is ~30m/s - (plane flies fine down to 11m/s with flaps retracted.)
Pitch is logged as 16-17, then drops a bit, level flight is normally around 0-1
Yes, throttle is low, but AS is plenty, still I drop like a rock, until in manual.

Also, my experience was that the plane pitched own, not up while losing altitude.
around line 403333 - I apparently fly without gaining altitude at 27deg pitch, 17m/s - this too seems just wrong.

IMU & IMU2 do not disagree , nothing is loose inside.
Also, EKF1.Pitch does not match ATT.Pitch - at all , and looks much more correct

Waypoint 13 has an altitude of 0. Every time it heads for that waypoint the plane dives down.
Thanks, Grant.

I an aware of that, please see around the mentioned line, or look up altitude drop, or pitch deviance vs ekf1.pitch