I know this is an old topic, but this (bug?) still persists in Java7u75.
I ran into the same issue... the solution offered by shambhu above does work, but results in a visible "window switching" effect:
stage.hide();
stage.show();
I found that the following code solves the problem (gets the stage to "refresh") without any visible effects:
final boolean resizable = stage.isResizable();
stage.setResizable(!resizable);
stage.setResizable(resizable);