Yes, I've noticed exactly the same problem. I went on a hike last week, that started and finished at about 200m and went up as high as 925m with a few other small ascents in between. I'd have guessed at about 900m of climb altogether, but my Vista HCx said 550m or thereabouts! The altitude plot on the unit looks OK, and the altitude plot displayed in OziExplorer from the downloaded track looked OK as well.
I'd be interested in what reply you get from Garmin.
My software is at 2.50 and GPS at 2.40.