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I installed JDownloader in ubuntu 11.10 with gnome-shell. Everthing works perfect, but when I 'm using JDownloader, it also creates an additional "window" called JavaEmbeddedFrame (the app with the java logo without window in this capture , if you select it from the dash or from the alt+tab menú it shows nothing. How can I remove that window?

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JavaEmbeddedFrame is a container for tray notification.

So if you don't want the empty window, disable Light Tray addon in your jDownloader settings.
If you used to use minimize to tray, then try Alltray app.

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