I noticed a book a moment ago with the backup application, it restores perfectly and everything but when you view your installed apps in android market they don't show because they were not restored via the market but via the SD card backup which is counted by the market as a 3rd party source.
What I had to do was go through each of the 41 apps in AppManager (free) and visit their market page then install them from there. No settings were lost, just an extra process if you want apps showing (and updating) from the market place "My Downloads" area.
Hopefully an update to the Backup Pro app will fix this for future use.