FULL PRODUCT VERSION :
java version "1.6.0_14"
Java(TM) SE Runtime Environment (build 1.6.0_14-b08)
Java HotSpot(TM) Server VM (build 14.0-b16, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Linux myhost 2.6.30-ARCH #1 SMP PREEMPT Sat Jul 4 11:13:08 UTC 2009 i686 Intel(R) Core(TM)2 Duo CPU T7500 @ 2.20GHz GenuineIntel GNU/Linux

EXTRA RELEVANT SYSTEM CONFIGURATION :
Archlinux
TwinView, two screens: the one with the tray is higher than secondary screen.

A DESCRIPTION OF THE PROBLEM :
Right-clicking the tray icon shows the popup menu incorrectly. The menu is outside of the screen, because it goes down (and I have system tray in the bottom of the screen).
The main problem is that the TwinView allows me to move mouse below the first screen up to the bottom of the secondary screen.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
You need to have two screens with TwinView. The one with the tray has to have the bottom higher than the second screen's bottom.
Put a simple popup menu to TrayIcon.
Run in Linux with the system tray in the bottom.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The popup menu is shown correctly, on the visible part of the screen. (All native components are able to detect this!!!).
ACTUAL -
The popup is not visible.

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
        if (SystemTray.isSupported()) {
            SystemTray st = SystemTray.getSystemTray();
            final TrayIcon ti = new TrayIcon(Toolkit.getDefaultToolkit().
                    getImage(Main.class.getResource("icon.jpg")));
            ti.setImageAutoSize(true);
            final PopupMenu popupMenu = new PopupMenu();
            popupMenu.add("Item 1");
            popupMenu.add("Item 2");
            popupMenu.add("Item 3");
            ti.setPopupMenu(popupMenu);
            st.add(ti);
        } else {
            System.out.println("NOT SUPPORTED!");
        }

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

CUSTOMER SUBMITTED WORKAROUND :
Move the screen so that both screen bottoms are at the same position.
Or create a class that extends java.awt.Popup, but renders the popup menu using the JPopupMenu.