question about adjusting Ardupilot

I tired my freshly built Ardu pilot today. I turned on my flight stablizor and then the ardupilot. When turned on the Ardu pilot in way point mode the plane immediatle went in to a turn and dive. Fearing for the life of my airplane I quickly turned the Ardu pilot off and recovered. After thinking about I few question came to mind. It might be have some thing to do with the altitudes in the way points. I have it set to 100 meters.. and I guess my question is this.. is the altitude in the ardu pilot calculating at sea level or ground level.

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