FULL PRODUCT VERSION :
java version "1.8.0_72"
Java(TM) SE Runtime Environment (build 1.8.0_72-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.72-b15, mixed mode)


ADDITIONAL OS VERSION INFORMATION :
Linux ron-Linux-Laptop 4.2.0-30-generic #36~14.04.1-Ubuntu SMP Fri Feb 26 18:49:23 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

A DESCRIPTION OF THE PROBLEM :
If a stage with transparent or undecorated style is shown on top of a full-screen stage, the transparent or undecorated stage is not visible, it seems to be hidden behind the full-screen stage.

It seems to work however if (1) the stage style is changed to StageStyle.UTILITY or (2) if the parent stage is not full-screen,

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1) create full screen stage and show it
2) create transparent or undecorated style stage (initialize the owner to the full screen stage) and show it


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
transparent or undecorated style stage content should be visible
ACTUAL -
transparent or undecorated style stage is hidden behind the full-screen stage

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
package sample;

import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.Label;
import javafx.stage.Modality;
import javafx.stage.Stage;
import javafx.stage.StageStyle;

public class Main extends Application
{
    private static Stage popupOwner;

    public static void main(String[] args)
    {
        launch(args);
    }

    public static void showPopup(ActionEvent event)
    {
        Stage popupStage = new Stage();

        popupStage.setScene(new Scene(new Label("This is a popup.")));
        popupStage.initStyle(StageStyle.UNDECORATED);

        //note: uncomment the line below and the popup is always shown
        //popupStage.initStyle(StageStyle.UTILITY);

        popupStage.initModality(Modality.WINDOW_MODAL);
        popupStage.initOwner(Main.popupOwner);

        popupStage.show();
    }

    @Override
    public void start(Stage primaryStage) throws Exception
    {
        Main.popupOwner = primaryStage;

        Button button = new Button("Show popup");
        button.setOnAction(Main::showPopup);

        primaryStage.setScene(new Scene(button,200,100));

        //note: set fullscreen to false and the popup with transparent stage style is shown
        primaryStage.setFullScreen(true);

        primaryStage.show();
    }
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
There is no workaround if a real transparent or undecorated stage is required.

One fallback solution is to use UTILITY style stages (which show a close button and a title bar).
Another fallback solution is to not initialize the owner of the transparent or undecorated stage but this will result in an automatic exit of the full-screen of the parent stage.