Jdownloader icon is giving some problem with the theme you are applying because it puts background color to the transparent icons. If you want it to look like compatible with your panel you must apply same background color with it. I did one for myself that is 24*24 and i am using equinox evolution light controls in my theme. When putting this icon in the folder /home/.jdownloader/jd/logo and replace with the old one your panel will be compatible again with jdownloader.