Bruce,
The altitude accuracy of GPS is notoriously worse than the horizontal accuracy. This is due to fundamental geometric limitations, but it can be exacerbated by poor satellite reception, so make sure your antenna has a clear view of most of the sky.
As an example, I have a nice little handheld Garmin receiver, which does very well for horizontal position but is quite often off by several hundred feet of altitude. Fortunately, it also has an aneroid barometer for measuring altitude. Interestingly, since it has no way of knowing the actual sea-level pressure, it gently calibrates the barometer over the long term by averaging the GPS-derived altitude data over time. This seems to work fairly well, and as a result it's always right to within a few dozen feet.
If you're sure your antenna is well-positioned, you might try averaging the altitude data over time.
Hope this helps,
Ed