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I have more or less the same configured like you.
The only difference is that I also added the options, that you have specified during the startup of the ntp daemon, to the rc.conf file.

So in details I have the following in my /nsconfig/rc.conf file.

ntpd_enable="YES"
ntpd_flags="-c /nsconfig/ntp.conf -l /var/log/ntpd.log"

Without the ntpd_flags the ntpd daemon is started without this options after a reboot.
Maybe this two options are the default values and they are also used without specifying it.
But just to be safe I have added them too to the rc.conf file.


Marco