This bugged me several weeks. Suddenly the icons of som applications did not display in the notification area in the system tray any more. They popped up with a tiny frame and were not removable, polluting my desktop.
The solution is very simple. You may only have one notification area. Ich you dare to configure another, it stops working. Even if you run two Xorg servers for two screens you have to remove all notification areas except one.
This is true for notification area 188.8.131.52 and maybe other - it probably depends on other gnome components too.