Can't transfer APPS from 3GS to iphone 5

just bought an Iphone 5 today and follow the instruction to restore from iTunes backup. Everything transfer except apps on the 3GS didn't migrate.  What I can do now?

Was the iPhone 3GS backup created after the apps were installed on the iPhone 3GS?
I've done this operation several times and it works.
Make another backup of the iPhone 3GS and restore your iPhone 5 using this new backup.

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