Nautilus Menu appearing behind transparent gnome-shell menubar

I installed Ubuntu 11.10 beta when it was released a couple of weeks ago. Everything is working fine.

Later I installed GNOME shell and then upgraded it from the gnome-shell testing ppa. I also installed and enabled all the gnome-shell-extensions available on the ppa. There is only one problem. When ever I switch to a theme which has a transparent gnome-shell menu I see nautilus menu behind it.

It only disappears when I quit nautilus. I don't know I to get rid of it so that I can use use themes like Nord and Malys properly.

That actually happens with the official Gnome Shell packages in Ubuntu 11.10 too (at least for me, at the time I'm posting this answer).

I only know a fix for this: disabling Nautilus from handling the desktop (so using this, you won't have icons on the desktop anymore). To do this, install "dconf-tools":

sudo apt-get install dconf-tools

Then launch "dconf-editor", navigate to org > gnome > desktop > background and uncheck the "show-desktop-icons" box.