Description of problem: The extension does not work with GNOME 3.6 while it worked fine with GNOME 3.4 and below.
This extension is disontinued... https://github.com/MrTheodor/gnome-shell-ext-icon-manager I will propose to remove it from Fedora. You can use TopIcon in replacement : https://extensions.gnome.org/extension/495/topicons/
Request to remove this extension asked: https://fedorahosted.org/rel-eng/ticket/5583