Comment 16 for bug 863309

I think Nautilus may have the same problem.

After the upgrade, Nautilus has sprouted menus when running in the root window.
The menus appear after about a short delay, just as in Gnome Terminal. Could there be a common cause?

I'm running Nautilus under fvwm (nautilus --no-default-window).

I've found one other reference to this problem, but no bug report:
http://askubuntu.com/questions/61105/nautilus-menu-appearing-behind-transparent-gnome-shell-menubar