FULL PRODUCT VERSION :
1.5 through 1.6, since setAlwaysOnTop option added to java.awt.Window

ADDITIONAL OS VERSION INFORMATION :
Windows XP, Windows Vista

EXTRA RELEVANT SYSTEM CONFIGURATION :
Replicated on several windows machines with both XP and vista.

A DESCRIPTION OF THE PROBLEM :
A JOptionPane owned by a JFrame which is not always on top can be obscured behind an always on top JFrame. Since the option pane is modal, you can't move the always on top frame to reveal it, so the application effectively hangs.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the test case program supplied

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The JOptionPane should probably be 'always on top' itself, so that it cannot be hidden behind the always on top frame.
ACTUAL -
The smaller always on top frame is in front of the larger normal frame. Since the JOptionPane is owned by the normal frame, it is obscured behind the always on top frame, and the UI hangs.

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
public class TestJOptionPaneAlwaysOnTopBug
{
    public static void main(String[] args) {
        SwingUtilities.invokeLater(
                new Runnable() {
                    public void run()
                    {
                        JFrame alwaysOnTopFrame = new JFrame("Test JOptionPane");
                        alwaysOnTopFrame.setSize(600, 400);
                        centreFrame(alwaysOnTopFrame);
                        alwaysOnTopFrame.setAlwaysOnTop(true);
                        alwaysOnTopFrame.setVisible(true);

                        JFrame normalFrame = new JFrame();
                        normalFrame.setSize(800, 600);
                        centreFrame(normalFrame);
                        normalFrame.setVisible(true);

                        JOptionPane.showMessageDialog(normalFrame, "Can't you see me?");
                    }
                });
    }

    private static void centreFrame(JFrame myFrame)
    {
        Dimension d = Toolkit.getDefaultToolkit().getScreenSize();
        int x = (d.width - myFrame.getWidth()) / 2;
        int y = (d.height - myFrame.getHeight()) / 2;
        myFrame.setLocation(new Point(x, y));
    }
}


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

CUSTOMER SUBMITTED WORKAROUND :
There is a workaround provided for related bug report 6578654, which involves creating the option pane directly rather than through the static convenience methods and setting the always on top to true - but I think this workaround needs to be incorporated into the standard JOptionPane static methods - it is a serious issue given that it totally locks the UI, and the cause of the lock up is not always obvious since the option pane remains invisible.