If you want to prevent the Show Desktop button from minimizing your transparent terminal, you may start gconf-editor and uncheck this value:
/apps/compiz/general/allscreens/options/hide_skip_taskbar_windows.
By the way, does anyone know how to start a gnome-terminal in a specific workplace? I want my terminal to be automatically launched in Desk 2 at startup, but I haven't found a way to do it.
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