I've been having altitude hold issues with Pixhawk.
I was previously using a Tarot 650 frame and altitude hold was near perfect. I transplanted everything from the Tarot 650 to a slightly larger frame. Same props/motors/ESCs/FC. Frame is nearly identical in weight. Motors are spaced slightly further apart on new frame. I've been using the RC TIMER plastic dome on both frames. Dome or no Dome there is not a significant difference.
I've been looking at the logs and it appears that GPS and BARO altitude agree and indicate the copter is descending.
I loose about 5 feet of altitude.