I've seen that happen, when nautilus has crashed, and is not there to provide the 'desktop' window. Nautilus has had a bunch of crashing problems in quantal, lately.
Are you experiencing any nautilus crashes? When you go to the empty desktop, does a right-click on the desktop bring up a menu? If it doesn't, nautilus has crashed.
I've seen that happen, when nautilus has crashed, and is not there to provide the 'desktop' window. Nautilus has had a bunch of crashing problems in quantal, lately.
Are you experiencing any nautilus crashes? When you go to the empty desktop, does a right-click on the desktop bring up a menu? If it doesn't, nautilus has crashed.