When you click on the "Shut Down"-applet button, the GNOME dialog containing the buttons [Suspend] [Restart] [Cancel] [Shut Down] opens (without the countdown timer working, not that it's relevant), and no matter which button you press except Cancel, it opens the Ubuntu Shut Down window with all the buttons.
Attempt to clarify:
When you click on the "Shut Down"-applet button, the GNOME dialog containing the buttons [Suspend] [Restart] [Cancel] [Shut Down] opens (without the countdown timer working, not that it's relevant), and no matter which button you press except Cancel, it opens the Ubuntu Shut Down window with all the buttons.