It is SOLVED. Maybe this might be helpful for others.
It appears that I am using Group as a root for my Scene. As said in JavaFX documentation: "If a Group is used as the root, the contents of the scene graph will be clipped by the scene's width and height and changes to the scene's size (if user resizes the stage) will not alter the layout of the scene graph".
Link: http://docs.oracle.com/javafx/2/api/javafx/scene/Scene.html