Motionbased has a feature that does some sort of adjustment when you upload. There's another feature you can turn on that adjusts even more (I forget what it's called). Personally, I don't think either adjustments are accurate at all. The unit readings are as close as you're going to get to actual IMO.

My guess is that the site does some sort of calculation differently, like using specs from the device compared to topo maps and things like that.