The dbus at_console code checks for presence of /var/run/console/$USERNAME to see whether the user is "at console".
In previous releases (don't know when it changed exactly) this appears to have been populated by libpam-foreground. Now there is a compatibility script /usr/lib/ConsoleKit/run-session.d/pam-foreground-compat.ck. This doesn't seem to get run with just a local console login. Running ck-launch-session explicitly seems to do the job.