Why don't I have my App Store apps after upgrading to iOS5?

I just upgraded my iphone to iOS5. Before upgrading I created a backup in iTunes. After upgrading I restored from backup. All of the apps I downloaded/purchased from the App store are now missing on my iPhone Only the core apps that come preinstalled on iOS5 are present.

However, all the music, contacts, and photos that were previously on my iphone are still there (ie the contents and settings in the core apps have been restored). Also, folders that I had previously put core apps into have been recreated.

Does this point to any error I made in the upgrade process? I didn't transfer purchases from iPhone to iTunes when prompted before the upgrade, nor do I sync apps between iPhone and iTunes. I assumed all this content would be included in the backup.