Comment 79 for bug 1532226

Multibrelch, it looks like that BAMF isn't properly initialized in your session. In fact, this could be the problem.

So, there are a couple of things you could try, to go further with debugging:
 1) Replace your /usr/lib/x86_64-linux-gnu/bamf/bamfdaemon-dbus-runner
      with http://paste.ubuntu.com/16046263/

Then try this for some time and see if this solve the issue for you.

If it doesn't, edit the file /usr/share/dbus-1/services/org.ayatana.bamf.service so that the Exec line is (so just drop the "-dbus-runner" sufix):
  Exec=/usr/lib/x86_64-linux-gnu/bamf/bamfdaemon

And again, give a test to this.

PS: I also noticed I did a mistake in the ppa version of the indicator (damned multi-editing!) so, something could have not worked because of that. An update should be available soon for you.