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 , if you select it from the dash or from the alt+tab menú it shows nothing. How can I remove that window?
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