The reason for this is that jfxrt.lib also has a class named JSObject. This JSObject does not have getWindow function defined while plugin.jar one has. If you change the dependency order of JAR and make java to resolve JSObject to plugin.jar then java is able to call getWindow function.
Following are the links to the javadocs of both the classes.Note that jfxrt one doesn't have getWindow defined.
http://docs.oracle.com/javafx/2/api/netscape/javascript/JSObject.html