Backup/Restore Missed Some Things

Had to swap out my iPhone 4 yesterday for a new one. I had been getting the "No SIM..." message multiple times. Before I went to the Apple store, I did a backup of the phone. When I got home with the new one, I did a restore, selecting the backup which I had just done. After the restore, it did a sync and loaded everything (music, photos, apps, etc) on the new phone. However, there were a couple of things missing.
The main issue was my wireless connections. I had 4 of them setup, but after the restore, they were all gone. I then noticed that the Exchange Server profile for my work email/calendar/contacts was gone. Had to redo that also.
I really don't remember if I went through this when I did the 3g -> 4 upgrade. It was the same scenario; backup the 3G, plug the 4 in and restore.
Did I miss doing something, or shouldn't the restore put the phone back exactly like it was when the backup was done?

UPDATE:
I discovered that iTunes did not recover ALL of the files on one of the backup DVDs I burned. I restored from the DVD again, using the "delete duplicates" option, and most songs seem to be back. I'm still missing about 100, but I suspect most of these are podcasts, which would have auto-deleted anyway.
FYI: Based on this experience, I STRONGLY suggest doing a library backup periodically, as a precuation. Using the iTunes backup option enables you to keep much of the metadata in your library (playlists and ratings, for instance). Copying your iTunes folder to an external HD as a double precaution isn't a bad idea either.

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