I am unable to prevent the closing of a stage on JavaFX for Linux. The attached sample application works as expected on Windows (it prevents you from closing the window, you have to kill it manually). On Linux, the window disappears but the process continues to run. In my actual application I also see this behavior accompanied by a string of GTK errors of the form:

(java:73103): Gtk-CRITICAL **: IA__gtk_widget_get_visible: assertion 'GTK_IS_WIDGET (widget)' failed

However, I don't see those on my test app so they may be a red herring.