Comment # 13 on bug 953954 from Raymond Wooninck

Can you check if the xembed-sni-proxy binary is actually running ?  If this
program does not run, then the old icons will not show up in the systray. 

What for me is strange is that it seems more an issue regarding "missing" icons
than that the systray is not working. 

If you interact with the blank space in the systray, do you see there then the
menu of pidgin, etc ? (e.g. doing a right click) ?