Updated apps on iTunes not syncing with iPhone 4S

Hello!
I've synced the iPhone 4S with iTunes 10.5, and in iTunes there are 53 apps with available updates (I'm choosing not to update some), but in the App Store app on the phone there's a badge saying there are 87 available updates. I've never experienced this discrepancy before. Some of the apps in the phone's Updates section of the App Store are apps that I've already updated in iTunes. So the sync doesn't seem to be installing them in the phone.
Any ideas?
Thanks.

Sure it's selcted, it's just not being stored in my iPhone's iTunes library as its stored on my macbook's iTunes library. I've dragged it to where I want it and it still won't store. I havne't needed to connect them with a cable since late last year I think with the new iTunes and updates, and you shouldn't have to. But this is frustrating, I finally found a way to get Tool on iTunes and I can't get it stored on my iPhone.

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iPhone 3GS Tech Specs: http://store.apple.com/us/browse/home/shop_iphone/family/iphone?mco=MTAyNTQzMjI

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http://support.apple.com/kb/HT5295
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Updated apps on iTunes not syncing with iPhone 4S

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