After backing up iPhone and then restoring, apps not restored properly

Hey guys,
I've noticed something that's pretty annoying with iTunes (latest version) and my iPhone 4. After doing a full backup, and then later a restore from that backup, all of my data gets transferred over properly except for my applications. I think that only certain applications get transferred over and my apps don't end up in the folders that I created on my phone before the backup and restore process.
Is this expected? It's weird that iTunes remembers my music, photos, contacts, and other settings but totally gets it wrong when it comes to putting my apps+folders exactly the way they were before the backup/restore.

I just had a similar problem with my 3G - I had done a full backup, and then later restored the backup. Everything was restored to my iphone except my apps. They all appear to still be on iTunes, but only a few were restored to the phone, and iTunes won't transfer any of the apps manually either. All are checked to sync, but none are doing it. Really aggravating.

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