FULL PRODUCT VERSION :
OpenJDK Runtime Environment (build 1.8.0_121-8u121-b13-0ubuntu1.16.10.2-b13)


ADDITIONAL OS VERSION INFORMATION :
Ubuntu 16.10

Works on Windows 10 correctly !

A DESCRIPTION OF THE PROBLEM :
You set a stage to fullscreen - works
Then you display any dialog (e.g. default alert dialog). Fullscreen is disabled and you see the Ubuntu menu bar and tray items (e.g. clock).

After you closed the dialog, fullscreen mode is active again.
See the code example below for reproduction.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
see code example


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Behavior like in Windows 10 (Fullscreen mode also if modal dialog is displayed)

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
  Parent root = FXMLLoader.load(getClass().getResource("sample.fxml")); //content does not really matter
        primaryStage.setTitle("Hello World");
        primaryStage.setScene(new Scene(root, 300, 275));
        primaryStage.show();
        primaryStage.setFullScreen(true);

        Alert alert = new Alert(Alert.AlertType.ERROR);
        alert.setTitle("Alert");
        alert.setContentText("Alert");
        alert.initOwner(primaryStage.getOwner());

        alert.showAndWait();
---------- END SOURCE ----------