Applications always transfer even when unchecked in itunes!

I have 2.2.1 firmware and i've just re-installed itunes hoping this would solve my issue, unfortunately it has not. Even though application sync is turned OFF in itunes applications installed from the iphone not itunes always try and transfer to itunes on sync, even though these applications don't ever show up at all in itunes. I've tried un-authorizing my computer then reauthorizing it after a friend suggested this. Syncing takes forever and is really beginning to bug the **** out of me.
Message was edited by: Zool_375

This is normal - any applications downloaded and installed by your iPhone are transferred (or should be transferred) to your iTunes library on your computer when syncing the first time afterwards. If you ever need to restore your iPhone with iTunes, you will need to re-download all apps again - either with your iPhone or with iTunes unless all apps are available in your iTunes library on your computer.
The same applies to any music purchased from the iTunes store on your iPhone - these songs will be transferred to your iTunes library when syncing the first time afterwards.

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