Let me clear something up for you, GDM is Gnome Display Manager Gnome is the Desktop Enviornment Metacity is the Default Window manager for GDE Compiz is the 3D Window manager Emerald is 3D window decorator
You would want to install Fusion Icon and add it to startup, It provides an easy way to access all the things related to Compiz. run the following command in terminal to install fusion icon sudo apt-get install fusion-icon if you do not have emerald then add *emerald* at the end of that line to install it then add fusion icon to the startup, command is fusion-icon and you know how to add it to startup ;) run fusion-icon it will place a small icon in the tray. use it to change window decorators on the fly. The problem happens because of Java, This pages might have solution for you http://linuxinside.blogspot.com/2008/01/solution-for-compiz-matlab.html
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