Hi folks, I don't know if this is a pidgin issue or an issue with the plugin.
I was using 12.04 with gnome-shell 3.4, and with the libnotify plugin enabled in pidgin, everything worked great. When I got a message, the notification popped up, and if the notification window went away, the icon would stop flashing once the pidgin message window was focused.
Now I've upgraded to 13.04, with gnome-shell 3.6, and the icon does not stop blinking when I focus the pidgin window. It only stops blinking when I very specifically go to the bottom panel, click the pidgin icon, and then click the body of the notification (not the x, not the "show" button).
If you need any information or if you think that this is not an issue with the extension, let me know. Thanks!