I would run portversion -v | grep "<" and make sure everything was upgraded
to start with.  If all the gnome and X11 related stuff appears to be
upgraded, it might be hard to track down which build was at fault.  I think
the gnome upgrade script made a logfile in tmp.  I would check to see if
there is one there and if so see what happened.  Did you have x11 running
when you tried the upgrade?  Did the machine reboot or simply logout?  

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