My bind install that came on the 6.1 installation runs from /usr/bin, whereas both the package and the source want to run from /usr/local/bin...
You should have named.conf in /etc/namedb unless there's something funny with the original install. Not sure if you need to run make-localhost script in that directory as I do it as a matter of principle each new system install anyway. If I update SSL/SSH/BIND I set the REPLACE_BASE/OVERWRITE_BASE knob (check the Makefile at ports dir for relevant knob name!) so the updated version will overwrite the older at /usr tree.
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