I have found two issues. 
Issue # 1.
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I have a frame & a dialog, which is launched using -Djava.security.manager, so that i can see the security warning icon. When both frame & dialog is visible. I press "start" + "D" button . So the all the windows on the destop gets minimized. Once again i press "start" + "D" button. So that minimized windows on the desktop , gets restored. Now the dialog goes behind the frame.  According to modality the modal dialog should be always above the parent frame. This can be reproduced from jdk 1.6.0 b104 , 6u10 &  6u11 b01 pit build.

Issue # 2 . 
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Repeating the same step of Issue # 1. When the modal dialog is below its parent. When i click on the portion of the visible dialog, the dialog dn't come above the parent frame. This happens only in 6u11 b01 PIT build. 

I tested the same scenario, using previous build like 6u10 b29 & b30. Clicking on the dialog the dialog come above the frame. Hence its a regression from 6u10 b30 to 6u11 b01.

Step to reproduce:-
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1) Run the below testcase.  
java -Djava.security.manager ModalityBug

2) ress "start" + "D" button . So the all the windows on the destop gets minimized. Once again i press "start" + "D" button. So that minimized windows on the desktop , gets restored. Observe that dialog is below the frame. If you see the same then the bug is reproduce Issue # 1 .
3) Click on the portion of the visible dialog. If the dialog dn't come above the parent frame , then the bug is reproduced. Issue #2.


============ Testcase ====================
import java.awt.*;

public class ModalityBug {

    public static void main(String[] args) {
        Frame f = new Frame("Test frame");
        f.setSize(200, 200);
        f.setLocation(100, 100);

        Dialog d = new Dialog(new Frame(), "Modal dialog");
        d.setLayout(new FlowLayout());
        d.add(new Button("b1"));
        d.setSize(200, 200);
        Button dbutton = new Button("Dialog Button");
		dbutton.addActionListener(new java.awt.event.ActionListener(){
			public void actionPerformed(java.awt.event.ActionEvent ae){
				System.out.println("dialog button is pressed");
			}
		});
		dbutton.addFocusListener(new java.awt.event.FocusListener(){
			public void focusGained(java.awt.event.FocusEvent e){
				System.out.println("Button gained focus");
			}
			public void focusLost(java.awt.event.FocusEvent e){
				System.out.println("Button lost focus");
			}
		});
        d.add(dbutton);

        d.setLocation(140, 140);
        d.setModal(true);

        f.setVisible(true);
        d.setVisible(true);
    }
}

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