Comment 4 for bug 1181189

That's weird. Just to make clear what you mean with "icon":

Whenever you start bt-autoconnect from the .desktop file (i.e. from its location in /usr/share/applications or from the "activities" menu) you can't access the application indicator's menu but when your run it from terminal with "bt-autoconnect" it works fine?

This should not make a difference as the .desktop file does nothing else but calling /usr/bin/bt-autoconnect script which in turn runs "python /usr/share/bt-autoconnect/bt-autoconnect.py".

Is this different behaviour when running "python bt-autoconnect.py" from a custom installation path?

Here on GNOME 3.6 all is as expected.