Comment 11 for bug 480030

Yes this fixed the problem. Pidgin is just doing what it was told to do.

If you uncheck the box by Pidgin > Tools > Plugins > Libnotify popups 0.14 then pidgin dissappears from the messaging menu. This is what is supposed to do. If you want to turn off the Libnotify pop-ups then highlight the entry and click the configure plugin button at the bottom. In the resulting dialog uncheck the boxes beside the notifications you don't want to receive. Uncheck them all and you get no notifications but you can still see pidgin in the messaging menu.