IPhone Apps won't sync to iTunes.

I need all my apps to sync to my iTunes for a complete backup. All the new apps I've purchased on my phone in the last few months do not show up on the apps tab in iTunes. I've hit the Sync button as well as Transfer Purchases. Each time the apps are said to be "copying" in iTunes but never actually transfer or appear in the apps tab. They're in the preview on the right, just not in the list on the left.
Sync Apps is checked, as well as Automatically Sync New Apps
I had the same trouble with the iPhone 3GS and had to re-download all my purchased apps when I upgraded to iPhone 4 because the backup I used to startup the 4 seemed to be incomplete.
It's as if iTunes won't update the backup file. It's stuck on a backup from a year or so ago.
Any ideas?

I'm also having this issue. There is no media folder with any apps files in my iTunes folder on my PC and so i can see all the apps in my library but they are all gray and have a "!" next to the app name because iTunes (nor myself) can't locate them.

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