Posted by gouessej on Jun 22, 2011; 11:01am
URL: https://forum.jogamp.org/KDE-task-bar-is-always-on-top-of-fullscreen-Java-applications-tp3088594p3095010.html

You tested with NEWT and this bug comes from AWT in my humble opinion. AWT should do this:
_NET_WM_STATE(ATOM) = _NET_WM_STATE_FULLSCREEN

If NEWT is not concerned by this bug, it does this thing somewhere. I'm going to look at the source code.

Edit: the solution is in https://github.com/sgothel/jogl/blob/master/src/newt/native/X11Window.c