Restore backup to iPhone 4S from iPhone 4 backup but apps are missing now.

I backup my iPhone 4. Then I setup my new iPhone 4S by selecting Restore from backup and selecting the backup of the iPhone 4 that I just did. When it is all complete, most of my apps that were in stalled on the iPhone 4 are not on my iPhone 4S. A few of the custom folders are there with only one of two of my downloaded apps but most are nowhere to be seen. I have rebacked up the iPhone 4 (which I confirmed still has all the folders and apps) and repeated the restore process but it turns out the same each time. Any tips? Thanks,
Marc

Figured it out. "Synch apps" was unchecked in iTunes.

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