Yep, I've had the exact same problem:
http://discussions.apple.com/message.jspa?messageID=7682228#7682228
It happened again this morning. Looking at newly posted apps in the store, I noticed Exposure had been updated. I went into my iTunes application folder and clicked the button to check for updates. It found three updates, but not Exposure. When you look at the app pages for these "updated" apps, some of them still show v1.0. But I let it download the updates anyway.
Version numbers between the app store page and using Get Info in iTunes don't match. For example, my iTunes app page shows v1.3 for Dizzy Bee, but when I look on the app store page it still shows v1.0.
And then iTunes was still insisting I had one update, although it couldn't find one.
After I updated the apps and synced, my phone still said I had an update, but it was for an app that didn't show up in the iTunes update page on my iMac.
And so on...
Message was edited by: blevenstein