I can confirm this bug with single monitor setup. The application is the game called Braid.
I don't want it to run Braid in fullscreen, because then it can't be controlled with window-manager (e.g. I can't minimize the game). So I start Braid in windowed mode with width and height equal to my screen resolution and compiz setup to remove window decorations for Braid and to show it in fullscreen. Everything works as expected, except that I still see the panel.
I can confirm this bug with single monitor setup. The application is the game called Braid.
I don't want it to run Braid in fullscreen, because then it can't be controlled with window-manager (e.g. I can't minimize the game). So I start Braid in windowed mode with width and height equal to my screen resolution and compiz setup to remove window decorations for Braid and to show it in fullscreen. Everything works as expected, except that I still see the panel.