My 0.02 is that the shiney new GPS of yours is using the WGS84 model of earth shape, or similar, which assumes the earth is an ellipsoid, or something like that. As I understand it, the GPS altitude read out is quite likely to be wrong due to this. From first hand experience, I can tell you that on the A330/40 for example, if you look at the GPS altitude on the FMS it is often out by over 1000'.