@Override
    public void start(Stage stage) throws Exception {
        final Button button = new Button("ABCDEFG");
        stage.setScene(new Scene(new Group(button),200f,100f));
        stage.show();
        Stage stage2 = new Stage();
        stage2.setTitle("Stage 2");
        stage2.setScene(new Scene(new Group(),200f,100f));
        stage2.initOwner(stage);
        stage2.show();
        
        stage.iconifiedProperty().addListener(new ChangeListener<Boolean>() {

            @Override
            public void changed(ObservableValue<? extends Boolean> ov, Boolean t, Boolean t1) {
                System.out.println("stage.inconified=" + stage.isIconified());
            }
        });
        
        stage2.iconifiedProperty().addListener(new ChangeListener<Boolean>() {

            @Override
            public void changed(ObservableValue<? extends Boolean> ov, Boolean t, Boolean t1) {
                System.out.println("stage2.inconified=" + stage2.isIconified());
            }
        });
        
        
        button.setOnAction(new EventHandler<ActionEvent>() {

            @Override
            public void handle(ActionEvent t) {
                stage.setIconified(true);
            }
        });
    }


Minimize the window using the trim, you'll get:
stage.inconified=true
stage2.inconified=true
stage2.inconified=false

Using, the button, you get the correct behaviour:
stage.inconified=true