This same thing is happening to me, did you find a solution?
My computer is authorized, apps will copy from itunes to my phone, and some will copy from my phone to itunes, but not all of them. the ones that won't copy to itunes don't even show up as being on my phone, yet i can see and use them on my phone fine. I've had the 3GS for a couple weeks and have never been able to get it to SYNC properly.
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