Confirmed. But I'm not sure this is a bug in unity or in openjdk.
Smaller code that reproduces this bug:

import java.awt.Color;
import java.awt.GraphicsEnvironment;
import javax.swing.JFrame;

public class ScreenTest extends JFrame {

        ScreenTest() {
                setUndecorated(true);
                getContentPane().setBackground(Color.RED);
                setDefaultCloseOperation(EXIT_ON_CLOSE);
                setVisible(true);
        }

        public static void main(String[] args) {
                
GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice().setFullScreenWindow(new
 ScreenTest());
        }

}

** Changed in: unity
       Status: New => Confirmed

** Also affects: unity (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: unity (Ubuntu)
       Status: New => Confirmed

** Summary changed:

- Full Screen mode for Java Apps
+ Top panel is shown over full Screen window for Java Apps

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https://bugs.launchpad.net/bugs/898121

Title:
  Top panel is shown over full Screen window for Java Apps

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