This is not a compiz problem. Pidgin must tell Compiz that it's iconified and 
not minimized, and it must tell Compiz where it's iconified to.
In rythmbox, this is done in the rb_shell_set_visibility function in 
shell/rb-shell.c.

** Also affects: pidgin
   Importance: Undecided
       Status: New

** Changed in: pidgin
       Status: New => Confirmed

** Changed in: compiz (Ubuntu)
       Status: Confirmed => Invalid

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pidgin minimize to tray is visually wrong using compiz
https://bugs.launchpad.net/bugs/146461
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