Loiter cannot get to desired altitude

After changing to Arduplane 3.7.1 and Pixhawk2, my airplane is having problems getting to the desired altitude on loiter.
I have setup a regular mission with takeoff, loiter to a desired altitude (up), survey, loiter to desired altitude (down) and land.

The problem first ocurred when the plane tried to get to the desired altitude (150m) at the first loiter: It went to the loiter position climbing, entered loiter at about 100m, got up to 143m and stopped rising (kept loitering at this altitude). After 5 turns, I activated the emergency command and it went to the landing loiter. (I loiter down to 90m before starting the land).
When it got to the loitering point, it was already at about 88m. Usually it should be at a higher altitude, not a lower one. This probably happened because of the unusual emergency activation. The airplane then entered the loiter and got down to 81m (it should have gone to 90m), and kept loitering for some time. After a couple turns it exited the loiter at about 80m and did the landing.

I also noticed that the airplane was about 7m lower in altitude at all the desired points, not just the loiters.
A fun fact is that 7m was the altitude at ground level.

The Arduplane runs on a Pixhawk2. This was my first time with the new Pixhawk2 (we used to go with the regular Pixhawk). The airplane, parameters and acessories were the same I always used.

I’m attaching the .tlog and the .log below

TLOG: .tlog download

LOG: .log download

Does anyone have an idea of ​​what might be the problem?

EDIT1: I just noticed that the .tlog shows me an altitude of 143m where the .log shows me a 150m altitude. Is this because of the ground level offset of 7m that I set? I was do my missions this away and it never showed that difference.

EDIT2: Forgot to say that the airplane fly in Auto mode the entire time.

this have something todo with different home-altitude sources.
fixed in 3.8. (currently a release candidate)

Does 3.8.0 beta6 has this corrected?