I think the App Store isn't synchronized in how all this rolls out. I've seen notice of updates when nothing appears at all. This morning I saw notice of an update on the iPhone that then showed it was already installed, meaning the version number posted didn't match the version number of the update.
In the second case, I looked the application up on iTunes, found notice there that the application had an update, but when I clicked on the application, it was listed as the old version. I downloaded it anyway, and it turned out to be a later version - an update after all.
I think this is all about timing of getting everything caught up. It eventually does get caught up, so long as I stop obsessing about getting the updates the moment they come out.