Why ipad reloads every single app when syncing?

I've had a really annoying problem and I don't know why it's happening. My ipad has iCloud back up turned on, but if I connect to itunes to add a new app for example, when I press apply, iTunes resyncs every single app on my ipad which takes 2hours or more.
What on earth is going on here? It never used to happen before iTunes 10, can't tell you how annoying it is, as it means i cannot manage my apps manually anymore.
Thanks

How to restore from backup without sync all my apps? I recently upraded firmware to IOS 7, and then tried to restore from my privouse backup. But it everytime, when it's saying you are successfully restored. but I when I unlock my phone all app icon are dark gray color, means nothing restored and then itunes automactically copying all my app to iPhone like 100+ apps, I dont need all of them.
Again, How to restore from backup without sync all my apps? 

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