Specification for Window.setLocationRelativeTo() states (at least for java 6):

   If the component is not currently showing, or c is null, the window is placed at
   the center of the screen. The center point can be determined with
   GraphicsEnvironment.getCenterPoint()

When the following code:

        JFrame frame = new JFrame("Invisible Frame");
        frame.setSize(new Dimension(300,300));
        frame.setLocation(0, 0);

        JDialog dialog = new JDialog();
        dialog.setSize(new Dimension(100,100));
        dialog.setLocationRelativeTo(frame.getContentPane());
        System.out.println(dialog.getLocation());


        System.out.println("Center point: " +
                GraphicsEnvironment.getLocalGraphicsEnvironment().getCenterPoint());


is run on sun jdk6 produces:
 java.awt.Point[x=590,y=350]
 Center point: java.awt.Point[x=640,y=400]
and when the same code is run on openjdk6:
 java.awt.Point[x=590,y=350]
 Center point: java.awt.Point[x=640,y=388]
[Note: gnome-panel is located on the bottom of screen]

As you can see graphics environment make a correction of center point, to
take into account gnome panel's size, but dialog is still located in the
center of screen, so specification is violated