I was looking through JMEDesktopState and was puzzled why the RootNode wasn't attaching either the desktop or the guiNode to it. It seems to be hangin' out on its own – is there are reason for this or is this a bug?
The desktop is attached to the GUI Node, which is rendered ORTHO mode.
The RootNode is just there for you to other 3D objects if you want, its not used by default.