Bre901 - that's a very interesting plot. For most of the time they are almost identical, but for one ten-minute period there is a difference of up to 300 metres. I wonder why? I think it is explained, but my schoolboy French didn't get the meaning...
Lowtimer - I see the altitude vary on my GPS III as well, however the variation is always (or at least seems to always be) inside the EPE quoted by the GPS (i.e. with a 15 ft EPE, you'll get 85-115 ft when you're 100 ft AMSL). I understand your second caveat as well, but i'm trying to work out if a GPS is reliable enough to highlight problems with an altimeter, or if any difference could just be a GPS wobble. I'm not planning on using it as a replacement