I have been continuing to look into this, wanted to provide some more information.

I checked my own paladin, and noticed a similar issue. If I go to the Statistics tab and look under Character > Gear > Mounts owned, it has me listed at 509 but my site has my paladin listed at 508. What's even more confusing is that if I look at my Mounts tab in-game, it says Total Mounts is 554. And then if I look at the armory for my paladin, it says 601. In short, I honestly have no idea what Blizzard is counting (or not counting) in each of those numbers, so it is very hard for me to deduce what might be going wrong.

I don't think I have time for it tonight, but I may try to write an in-game addon or script, that will loop through the Mounts tab and try to compare it against the data my web site has. Again, my hunch is that if we compare mounts side-by-side, things will match except for the two new store mounts. I think Blizzard is just kind of inconsistent with how they count their total in-game. We'll see!