Nathan,

GPS is not nearly as accurate in the z dimension as in the horizontal
dimension. I often see mine (even with WAAS corrections) differ as
much as 3-400 feet from my altimeter.

Reference for your altimeter is a pressure level (hence it's called altitude
and not height), reference for GPS height is an approximation of the earth
called the "geoid", usually in form of WGS-84. I'm not sure if WAAS takes
this into account. If not the difference is system immanent.

Regards

Kai Glaesner