Okay, this is slightly weird. If I move that out the Prefs folder, the wallpaper goes back to Aurora, however, if I try and add a custom folder again, it adds it as a second "Aperture Projects" - and I still can't see any actual folders.
So I now have, again, two Aperture Projects things, one of which opens into a menu with the Aperture stuff in it, and the other doesn't do anything.
Maybe Aperture is screwing it up?