Perhaps your barometer is getting faked by higher pressure when travelling at higher horizontal velocity. A test method to see if this is happening would be to set Alt Hold mode and fly manually at high speed and see if altitude droops during transit and bobs up on hover. Also, you could try a mission with WP's closer together and with WP speed ( ie. WP_SPEED_MAX) set lower to say 3-4 m/s.
I have a APM 2.0 which hides the baro under the daughter board but I think a lot of APM2.5 users are putting cotton pads on their barometers to avoid errors due to turbulence.
i have cotton gauze over the barometer, and fly wp's at 2.5 m/s. In Alt hold i can fly all around the field at a pretty good click, and it will hold alt. within a couple of meters, even when i stop it stays close. Close wp's keep it from hitting the ground, but i'd be nice to do a long wp without descending. even if i set the default alt and wp alt. to say 20 meters, it only makes it up 4 or 6 meters. if i manually take it up to 20 or 30 meters it will descend to that 4 or 6 and start the mission and start its slow decent between wp's. Its crazy i know.