I am using pixhawk copter for auto missions. there is a slight difference in the desired altitude from waypoint. The given altitude is 50 meters but pixhawk sets the desired altitude as 49.23 meters. and in another mission I have given 142 meters as relative altitude from the home but pixhawk sets 146 meters as desired altitude.
Your main problem imho is the vibration to the board (check the IMU2), the second a bad tuning of the rate controller, especially on the roll.
Please also check the little sponge over the barometer.
But first tries to reduce the vibrations of your copter.
thank you @marco3dr… Is that possible that the change in altitude due the untuned setup or vibration. But will it cause the pixhawk to change the desired altitude?
My point is vibrations and untuned setup can cause the copter to not to fly in the desired altitude but will it change the Desired altitude?