I'm sure I've read somewhere a reporting for that same bug, but then the user got it solved on his own without letting know how he did it.

Anyway, that's what happens. When I use gnome-tweak-tool to set Nautilus to manage the desktop gnome-shell will break transparency in the activities overview. The translucent black background where you could see the background image will simply turn black. I also confirm that only happens if nautilus manages the desktop; as soon as I disable this feature gnome-shell will come back to normal but... while getting back the translucent background it will still keep the black background until I manually change the wallpaper from screen settings.

I've also read on forums of people with the same issue and they were told it's their gnome-shell theme that has been broken and they should fallback to the default gnome-shell theme. Others said that it's the video driver's fault. They're all wrong; I've just made a minimal graphical desktop installation through the Fedora 18 netinstall disc in VirtualBox without installing any extension nor gnome-shell theme so I can assure you they have nothing to do with this issue; if they had, the gnome-shell activities overview would be broken since the beginning, which doesn't happen.
I don't know if that's of any use to you but In past I remember this issue has been experienced with gnome-shell 3.4 too (or probably 3.5) by some users (I didn't). The same feature though works fine on a Fedora 16 installation (with gnome-shell 3.4).

Now, I'm also unsure if this is a nautilus or gnome-shell issue. They're both involved in this but I have no idea how to identify which one is causing the issue. So I posted this a gnome-shell bug since it should be gnome-shell managing the translucent background while nautilus should only draw the desktop (which actually does it). Sorry if I'm wrong...
I would attach you some logs but I'm unsure which could be helpful to you. I'll be waiting for any log request you may have.

Please solve this issue as soon as possible because I hate not having files on my desktop, and I hate the black background too, as same as many other users out there.

Thank you for your attention.