After the fix for 6380835 all the java.awt.Windows was made non-OVERRIDE_REDIRECT. I have found a case that was not covered with the fix: usage of tray icon's tooltip, on X. In XTrayIconPeer a class InfoWindow is defined. It is a subclass of java.awt.Window and is used for displaying icon's messages and tooltip. As it is no longer OVERRIDE_REDIRECT, it appears below the taskbar where the tray is located. It is reproducible at least on my KDE 3.5.4.

To reproduce the bug run any test that creates a tray icon and sets a tooltip for it. The move the mouse over the icon and wait until the tooltip is shown. If it appears below the taskbar, the bug is reproduced.
it's not reproducible on KDE 3.3.2