Copter losing altitude in guided mode at constant desired altitude with RTK GPS as EK3_ALT_SOURCE

I am using arducopter 4.1.0-dev master version on omnibusF4SD running omnibusf4pro firmware on a quadcopter with Here+ RTK GPS. I am taking RTK GPS as primary EKF3 ALT source by setting EK3_ALT_SOURCE to 2. Also, I have kept EK3_ALT_M_NSE to default i.e. 2. I managed to get RTK float with base station accuracy of about 0.5 meters and flying drone about 50-60 meters of range from base station.

I am flying my quadcopter in guided mode and running a mission where i am giving navigation commands to quad to maintain the constant 4 meters altitude during the whole flight. In my recent flight with this quadcopter, after takeoff my drone started coming down slowly during the flight and lost 2 meters altitude, made an altitude drift/change of almost 2 meters.

When i checked the log i saw something which was not right , my GPS.Alt was not changing as the drone started coming down, but my baro altitude showing right log graph where it can be seen that drone does declining upto some point then maintained a constant altitude of around 2 meters in real time but POS.alt showing it maintain altitude of 4 meters.

I am attaching the log below:

I faced exactly similar issue recently on pixhawk as well with exactly same setup, i made a post about that but haven’t got any response yet. This was the earlier post: