@tridge, you asked for logs showing GUIDED fly back up with the flaps down.
I just did this today,
http://marc.merlins.org/tmp/12_GUIDED_FLAPS_CLIMB.BIN
At 3:22, I disabled geofence, used MANUAL and put full flaps to drop below 100m,
https://youtu.be/NgUKE-YJfHg?t=3m45s
guided takes over and climbs back to 100m
So that’s good 
What’s not so good was that my fence return altitude was 150m, and it only went back to 100m
PARM, 651332702, FENCE_ACTION, 1
PARM, 651332718, FENCE_TOTAL, 6
PARM, 651332734, FENCE_CHANNEL, 8
PARM, 651332839, FENCE_MINALT, 100
PARM, 651332855, FENCE_MAXALT, 1000
PARM, 651332870, FENCE_RETALT, 150
PARM, 651332886, FENCE_AUTOENABLE, 0
PARM, 651332902, FENCE_RET_RALLY, 1
I did not have a rally point, so it went back to the takeoff point, which is good, but ignored the 150m and went back to 100m.
Any idea why?
Then, there are clear issues with airspeed, but I put that in another message: Why does airspeed not reset to 0 before takeoff and why did autocal make it worse?