I have problem with authentication when an application needs root rights, for e.g nemo mount partitions gives error "Authentication error". I'm using fluxbox and I have install dbus, consolekit, polkit and polkit-gnome as authentication agent. I added in fluxbox startup script /usr/lib/polkit-gnome/polkit-gnome-authentication-agent-1 but seems that doesn't work. I tried also to run it from terminal and I get an error about consolekit session(sorry I don't remember the exact error and I am not in obarun now, because lot of stuff need to be configured and work). I use this in .xinitrc as cmd:
exec ck-launch-session dbus-run-session $@
to start it.