@adam65535:
It looks like it is working properly now adding -U 0 to both the system.inc and ntpdate_sync_once.sh script.
Great, I'm glad it works! Since the forum where this was first discussed is closed (2.1 beta feedback, https://forum.pfsense.org/index.php?topic=62099.msg341908#msg341908), can you post a short note to redmine: https://redmine.pfsense.org/issues/3045 This is a crutch rather than a proper fix, but it should be a big clue to the devs who can do a real fix. That's above my pay grade though :)
Interestingly I don't see the -U 0 in the freebsd man page doing a google search.
Dynamic interface scanning has been in ntpd for a while, since about 2006: http://bugs.ntp.org/show_bug.cgi?id=622