Version: (using KDE 4.2.2) Installed from: Compiled From Sources When using auto-hiding panels with the "Fade" effect, the panels are forced below the fading window for the duration of the animation. (Defeating one of the purposes of the fade: to provide a more relaxing user experience by removing as many perceptually instantaneous changes as possible) The simplest way to test this is to put your system tray in an auto-hide panel, move a window with a tray icon so the panel overlaps it when visible, and then click the tray icon to hide the window. I've tested it with Audacious Media Player 1.5.1 (GTK+), X-Chat 2.8.6 (GTK+ with a differently-implemented tray icon), BasKet Note Pads 1.0.2 (KDE 3.5), and Kopete 4.2.2 (KDE 4.3) to confirm that it's not specific to a given tray icon implementation and I've confirmed that there's no visible suspension of panel-on-top with "Fade" disabled.
*** This bug has been marked as a duplicate of bug 158262 ***