I have one of those annoying intermittent problems. Occasionally, when I boot Sabayon 9 into the Gnome 3 gnome-shell environment, nothing on the desktop works except the mouse pointer. The Super key will not activate the application doc, and clicking on the top panel icons does nothing. I can always work around the problem by pressing the F Lock key, then Ctrl-Alt-F1, then logging in as root in the test console, then running "/etc/init.d/xdm restart". Then I have to log in again as the normal user, and then everything is working again. An alternative workaround is to reboot the system.
Does anyone have any idea what is happening and/or how to fix it?
Tim


