Comment 53 for bug 491521

Well, notice that it isn't all the applications that have a tray icon that fail. Empathy, Gnome-Mplayer, nm-applet, gnome-power-manager, gnome-volume-control-applet, Rhythmbox, Padevchooser, Gmpc, Tomboy, and Nautilus (the tray icon comes up during large file transfers, deletions, etc) DO work for me. It may be something wrong with my system, so I'll double-check with a fresh install, but I highly doubt it.

A possible reason for a problem might be apps setting their own global colormap to an rgb one, which is relatively easy to look for like the problem in gksu. Some might also be using TrayIcon instead of GtkStatusIcon, which may be the cause this problem for some.

Another problem I encountered was flash not working in Midori, Epiphany, or Chromium. It did work in Firefox though. This may not show up in Firefox because it embeds flash differently due to actually having the windowless mode working.