FULL PRODUCT VERSION :
java version "1.6.0_03"
Java(TM) SE Runtime Environment (build 1.6.0_03-b05)
Java HotSpot(TM) 64-Bit Server VM (build 1.6.0_03-b05, mixed mode)


ADDITIONAL OS VERSION INFORMATION :
Linux macdonaldjlinux 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 x86_6
4 x86_64 x86_64 GNU/Linux

A DESCRIPTION OF THE PROBLEM :
When you show a modal JDialog in a Java application on Linux, it causes all the other JFrames (not just the parent JFrame) to appear in front of native windows. For example (ascii art):

+--------------+
| jframe1 |
| +---------------+
+-| native window |
  | |
  +---------------+
  
+--------------+
| jframe2 |
| |
+--------------+

If you launch a modal JDialog from JFrame2, then JFrame1 will pop in front of the native window. This is incorrect -- JFrame1 should stay where it was. This did not occur with Java 1.5.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the attached program, DialogTest, using Java 1.6, on Linux (doesn't occur on Windows).

Two frames will appear, Test1 and Test2. Place Test1 behind a native window (e.g., a terminal window). Now click on the button in Test2. This will launch a modal dialog.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The frame "Test1" should remain behind the native window.
ACTUAL -
The frame "Test1" pops in front of the native window.

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import javax.swing.event.*;

public class DialogTest
{
   public static void main(String[] args)
   {
       JFrame f = new JFrame("Test1");
       f.addWindowListener(new WindowListener() {
               public void windowActivated(WindowEvent e) {
                   System.out.println("windowActivated(" + e + ")");
               }
               public void windowClosed(WindowEvent e) {
                   System.out.println("windowClosed(" + e + ")");
               }
               public void windowClosing(WindowEvent e) {
                   System.out.println("windowClosing(" + e + ")");
               }
               public void windowDeactivated(WindowEvent e) {
                   System.out.println("windowDeactivated(" + e + ")");
               }
               public void windowDeiconified(WindowEvent e) {
                   System.out.println("windowDeiconified(" + e + ")");
               }
               public void windowIconified(WindowEvent e) {
                   System.out.println("windowIconified(" + e + ")");
               }
               public void windowOpened(WindowEvent e) {
                   System.out.println("windowOpened(" + e + ")");
               }
           });
       f.setSize(300, 200);
       f.show();

       final JFrame f2 = new JFrame("Test2");
       f2.getContentPane().add(new JButton(new AbstractAction("Push Me") {
               public void actionPerformed(ActionEvent e) {
                   JDialog d = new JDialog(f2, true);
                   d.show();
               }
           }));
       f2.setSize(300, 200);
       f2.setLocationRelativeTo(null);
       f2.show();
       
   }
}

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

CUSTOMER SUBMITTED WORKAROUND :
Use Java 1.5; make dialogs non-modal; have not tested alternate window managers.