Well... this is a really dumb post but I just discover this a few minutes ago and maybe can help someone else. If you are running jdownloader in ubuntu or any gnome linux platform maybe you noticed that by default the theme is java metal. I don't dislike the theme but this have some issues with compiz, for example sticky windows simply doesn't work and sometimes you can't maximize. In the other hand always is nice having an unified look and feel for all apps.
You can open JDownloader, open preferences tab and select interface node. In theme option you should select "Light(GTK)" and restart JDownloader. That's it now JDownloder behavior and "look and feel" is just like any other Gnome app.