Bug found in Fedora 18, and already mistakenly reported at the GNOME BugZilla: https://bugzilla.gnome.org/show_bug.cgi?id=694548
/var/lib/PackageKit/prepared-update needs to be erased as the system reboots.
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.