GPS altitude
Amongst other things, my old Garmin GPS III (non-pilot) tells me my current altitude - assuming it has found a certain number of satellites; if not, it switches to 2-D mode and the altitude display disappears. Sitting on the ground it seems to do a good job - both the figure in Pooley's and the altimeter (with the aerodrome QNH set, of course) are within the estimated position error on the GPS (around 15ft).
Now assume I'm at 2500ft (on the altimeter) doing 80kts. The GPS is still tracking a reasonable number of satellites, the EPE is not significantly different to the value on the ground and we're still in 3-D mode. Would you expect the GPS to still agree with the altimeter. If not, why not - and if the difference is significant which is more likely to be in error?