In reply to Heike:
How often is it recording the altitude? Does it have any settings to smooth the recording out?
I've an old Garmin forerunner and you can choose the frequency the GPS records at - mine just has two options, every second and smart which records less often thus should give a smoother profile.
Also, have you tried looking at the data? Is it really spiky
Personally with all GPS devices I ever only trust the position, the altitude unless it's barometric, is generally a bit rubbish. In the UK our weather changes rapidly, meaning you'll often need to recalibrate an altimeter several times a day. On a short run this should be less of an issue but on a full hill day changes in pressure as weather systems move can make a big difference.