I still don't know why but many GTK+ applications use something called eggtrayicon. As far as I know, eggtrayicon.c is a file written in 2002 by Anders Carlsson which implements the Freedesktop.org system tray procotol for GTK+ applications.
Problem is that this C file is used in dozens of programs and maybe more, and is a bit bugged. I've already send patches for mail-notification and Audacious. pidgin is the first fixed implementation I found and works quite well. Many other applications are probably affected.
That seems to me like a real problem. Multiple copy of bad code instead of using native GTK+ system tray implementation.
So please stop using this bad implementation…