I just tried to fly some test flightlines using 3.8.0, all waypoints for the flightlines were set to 122 meters. When I switched to auto mode, the plane was close to 122 meters altitude, it turned for the first waypoint and descended, reached that waypoint, turned for the next waypoint and continued to descend, it was down to around 30 meters altitude when I took over, right after that, I got some altitude back and then switched to RTL, it turned for the home waypoint and climbed to 100 meters, which the RTL altitude was set to, so RTL worked exactly as it should.
I checked the telemetry log, and all flight line waypoints were set to 122 meters, so have no idea what caused this, has anyone else had this issue with 3.8.0 so far? I am running a Pixhawk 2.1 with 3.8.0.