Upgraded to 5.0, restored from backup and see no apps

I decided today to upgrade to iOS 5.0. I first transferred the apps, did a backup and went ahead and told it to upgrade. After the process, I noticed I had a bareboned iPad. Just the stock apps and none of mine. I then did a restore from backup and it's the same situation.
Why didn't the restore bring back the apps?
Now I have to download them agian from the AppStore

All apps on your iPhone should be in your iTunes library on your computer - along with all other iTunes content selected to be transferred to your iPhone. iTunes content is not included with your iPhone's backup including 3rd party apps. After downloading an app with your iPhone, the app should be copied to your iTunes library on your computer the first time you sync your iPhone with iTunes after doing so - the same after purchasing music with your iPhone.
You can re-download an app with iTunes on your computer and you won't be charged again for a purchased app as long as you use the same iTunes account to re-download the app that was used to purchase the app originally.

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