Step to reproduce:
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1) Run the attached program. You can see the TrayIcon is added to the SystemTray. If you dn't see the TrayIcon, Click on the 'SetImage' button. A file dialog appears, select any one of the image file that is atached(animdog.gif & cupanim.gif). now you can see the selected image as TrayIcon.
2) Click on 'Toggle Popup' button.
3) Right click on TrayIcon , you can see a popup menu above that SytemTray which does not
match with the native popupmenu.

I have attached two screen shot(SystemTrayPopupMenu.png & Nativepopupmenu.png). You can observe that the java popupmenu(SystemTrayPopupMenu.png) is not matching with native popupmenu(Nativepopupmenu.png).

Note:- Please see SytemTray bug 6400191 ( Vista: SystemTray's popup menu is placed 50 pixels above the taskbar) for placement of popupmenu.

I tested this on Vista beta2 (build 5308) on Mustang b76.