Wallpaper custom folder and Aperture
I had the same problem and was very confused... until it unexpectedly went away when I re-created my iPhoto library so I could open iPhoto to help a friend find a menu option...
Another symptom I had in the initial problem was that the Aperture library appeared twice in the list of folders on the left of the Desktop Picture preference pane there were 3 categories: Apple, Aperture and Aperture (the first 'Aperture' could not be opened however).
Anyway it seems that the first non-working 'Aperture' section in the left slider may have been my old 'iPhoto Albums' section, and was now broken due to the iPhoto library no longer being present. So recreating it (I probably used the same (default) name, not sure if it has to be identical) may have solved the problem. Furthermore, there may be a 'safe' way of deleting the iPhoto library that properly records it in the Desktop Background preferences so that this doesn't reoccur... If I figure that out I'll make another post, but for now just having the iPhoto library back in place (but empty, in my case) has solved the problem for me.
