I'm not sure if anyone has the same problem. It can be a problem of my own system, as I didn't find any signs of it in Google, that's why I'm not sure if it's worth a bug report.
Preconditions: Pidgin is added into tray whitelist; showing mode "Always" in enabled for tray icon. I'm running Ubuntu 12.10 with Unity, Pidgin v.2.10.6.
My actions: 1) Verify that Pidgin icon is visible in tray. 2) Open a full-screen application (in my case, those were Wine or SMplayer) 3) Switch back to any non-full-screen app using Alt-Tab.
And the Pidgin icon disappears from the tray. To enable it again, I switch 'Show icon in tray' property to any other mode, and then back to 'Always'. Can anyone reproduce this problem? What configuration files and/or logs should I look into?