Altitude issues with Pixhawks

I can have one auto flight with my plane where it follows the programmed altitude perfectly and the next it flies way too high and pitches up and down randomly.

I have 2 planes with Pixhawks and the problem is the same with both. Flights are programmed terrain following and I check all the terrain maps are loaded in the status option.

There seems to be no pattern to when it happens.

Sometimes when in Mission Planner my altitude on the bench holds perfectly with a varience of a meter or 2, but sometimes it slowly climbs to over 15 meters and back for no reason. Again, same with both Pixhawks.

Any ideas?

Do the altitude changes persist when not following the terrain map?
Do the altitude issues still happen when flying manually in Alt Hold mode?
Have you added the open cell black foam over the BARO chip inside the case?
Can you post the log from one of the erratic flights?