freebsd-update upgrade -r 12.0-BETA does not execute pwd_mkdb.
If we are using ntpd on 11.2-RELEASE or before, freebsd-update upgrade adds ntpd/ntpd to user/group but does not execute pwd_mkdb.
So we must execute 'pwd_mkdb -p /etc/master.passwd' by hands.
This bug makes upgrading the system with source impossible since `make installworld’ now checks for the presence of the ntpd user (with uid tool).
Running the command given in comment #1 prior to installworld fixes it.
This still seems to be an issue with upgrades using freebsd-update. I updated to, if I recall correctly, 12.0-RC1 several weeks ago and got an error on boot "pid file /var/db/ntp/ntpd.pid: Permission denied". The directions above fixed it. I skipped RC2 and updated to RC3 today from RC1 and got the error again. I have another system I've been updating via source, and I haven't had this issue on the source-based system.