A late followup here... Did you get this figured out?
I've been meaning to try this for a while and I just now went through Doug's article at
http://www.vansairforce.net/articles...g/GPSTrack.htm and it worked for me.
A couple of things: In MapSource, in the Tracks tab, double click on a track to get the Track Properties window. If that shows correct altitude for each point in the track, then your 496 is recording altitude and that's not the problem.
In the current version of the GPS Visualizer page, you have a choice to Add DEM Elevation Data. Say "No" to that, otherwise altitude data in the track will be lost.
Anyway, if you gave up before, try it again and see if it works now. It does for me...
--Paul