Altitude Initialization

I have seen consistent differences between an inputted AGL (above ground level) value when producing waypoints and output from laser rangefinder (Lightware SF11/C) during a flight, which are on the order of about 20m. I am suspicious that this error may be coming from an altitude initialization occurring before takeoff.
I am wondering if / how an altitude initialization occurs and possibly where it occurs in the ardupilot source code? I have been trying to look through it myself but have had no luck.



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