My x4 quadcopter with Pixhawk is losing altitude when traveling between waypoints in Auto mode. Once it gets to the next waypoint (where it is told to delay 2 seconds), it regains the altitude it was supposed to be in through the path. This goes on between many waypoints placed in a line, as can be seen in the screenshot taken from the KML of the flight. I am attaching graphs of my barometer alt and the gps's relative altitude. How can I fix this problem? 

Thank you for your help.

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Thanks for your suggestion James. My altitude hold P gain is already at 1.00. Mission Planner does not let me raise it above 1.00.

hint:  posting a .BIN log could actually enable somebody to give you the answer. (unless you prefer wild guessing)  :)

Thanks!

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if you plot CTUN.BarAlt and BARO.press   , you can see the sensor does clearly see the pressure increase as it descends.

So it's not wind/speed influence, but tuning.

I'd suggest you upgrade to current release, and compare your settings to defaults, keeping only offsets, modes, stab and rate PID's and other known-to-be-good parameters.  - then try to tune it from there.

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