App organization in iTunes does not transfer to iPhone

I have an iPhone 3G and just purchased a new Mac Pro. I successfully transferred all my songs and apps from my old Mac to the new one. However, when I synched my iPhone for the first time, it placed all of my apps in alphabetical order (except for the native iPhone apps on the first screen).
I used iTunes to arrange the apps back the way I wanted to, but when I clicked "apply," it synched the phone and put them all back the way they were on the phone (alpha order). I used to be able to arrange apps on my computer, then transfer that setup to the phone.
This doesn't seem to work anymore, and I can't figure out why.
Any help would be appreciated.
Thanks,
-ME

I highlighted the albums that hadn't tx and then <command i> (get info) assigned a genre to each album, then clarified the sync instructions to include entire music library, then everything went over.

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