This looks like a packaging error -- gnome-session is looking for gconftool-2 in a directory that only existed at the time gnome-session was built.
Gnome is maintained by a team, rather than an individual. Antoine Jacoutot (ajacoutot@) has made all of the recent commits for gnome-session. If these warning messages on exit cause concern, or causes gconf processes to hang, you could always post about them to the ports@ mailing list, or send a note to Antoine.
It is possible that Antoine or another developer could produce a -stable port with a fix.
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