Do you only have the single itunes account? Also have you changed the default location that you used to store the music and apps on your computer? There is a problem with itunes, where if you change the storage location, it will store apps in a different location to everything else. So apps continue get stored on the default c:, and everything else gets stored in your other location that you setup. Really annoying I find. If you look in those folders you should find all your apps and music. If not, then it wouldn't have synced properly initially prior to you doing the backup.
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