Please run the following test:

import java.awt.*;

public class VisibilityTest {

    public static void main(String[] args) throws Exception {
        EventQueue.invokeLater(new Runnable() {
            @Override
            public void run() {

                Frame frame = new Frame("Frame");
                frame.setBounds(50, 50, 100, 100);
                //frame.setVisible(true);

                Window window = new Window(frame);
                window.setBounds(300, 300, 100, 100);

                window.setBackground(Color.blue);

                //Frame other = new Frame();
                //other.setVisible(true);

                window.setVisible(true);

                try {
                    Robot r = new Robot();
                    r.delay(5000);
                } catch (AWTException e) {}

                window.dispose();
                frame.dispose();

                //other.dispose();
            }
        });
    }
}

On Windows I can see the window (blue square) when the parent frame is invisible; on Linux - can not.

JDK version: 9 b20
OS: Windows 7 / Ubuntu 14.04

The window become visible on Linux
1. if the parent frame is visible (please uncomment 'frame.setVisible(true);')
or
2. if uncomment the code concerning 'other' frame - that's weird because it does not have any relation to the window.