I did a Backup recently (so I could "Restore" it onto a 2nd Genos) ... and I too only saw the .bup file, and the Audio filter. All was OK though, and my backup file did indeed have my Voices, Registrations, Multi-pad setups, Songs, etc. Remember that there is a limitation of up to 2 GB only for the Backup (not including Audio files), per the Referene Manual.
So, it would seem that the .bup file is a special kind of file, that "internally" has all your folders for your stuff such as your custom Voices (not Expansion voices though), your Registrations, your Multipad setups, your Songs (MIDI), etc. etc. - everything except your Audio files. Oh and the .bup must somehow have your MIDI settings, as when I restored to a 2nd Genos, it automatically got my customize MIDI settings.
Jim