Regardless of how many times I've clicked in iTunes to check for updated apps, it still shows a badge of 2. Even when new updates come out, that number goes up, they get downloaded, and it comes back to 2. Any way to fix this?
The way apps are currently handled in iTunes is badly broken, I would suggest completely ignoring iTunes and just handle installing/upgrading/deleting apps on your iPhone/iPod Touch instead.
You should just have to sync iTunes and the iPhone/iPod Touch and everything should get reset. Or try right clicking on Applications on the side bar and see if there is a menu option to reset.
You may also need to tell iTunes to check for purchases, as there may be a hitch it their giddy-up.
I was having trouble with the updates initially, but lately they have been working well. I don't know if it's related to 2.0.2, but I think I have seen some improvement.