I've had this issue as well -
In my iTunes on Snow Leopard (10.6.2) and iPhone 3G 3.1.2, the apps badges show updates available,, but when i go to download the updates or see what they are it's the same two or three apps
I've downloaded the updates several times but the badge still reads "unread" and the same apps are always listed. Any suggestions about what to do?
(The apps are "remote" + "mover" + "local concerts", i know it's not the apps though as it was just 2 prior to today when a new update for remote came out and now it's all 3 of them)
I've got mild OCD for this and it's doing my nut in!