Alright, I've managed to solve the problem by switching from OpenNTPD to the "not open" regular NTP. I'll document in here for future reference.
First off, check which tree is OpenNTPD running on (default is "root") with colour (-z) and in graphical form (-g):
# 66-intree -zg
Next, disable and stop OpenNTPD within your appropriate tree (the commands below
assumes that the root tree is current):
# 66-disable openntpd
# 66-stop openntpd
Next, you'll need to install "ntp" and "ntpd-66serv" via pacman, yay, etc. Optionally to prevent bloat you can remove "openntpd" and "openntpd-66serv".
In my case where the hardware clock is stuck in February 2013, I need to modify the default values in the script through 66-env (i like nano)...
# 66-env -e nano ntpd
...with force sync (-q) irregardless of the time gap between my system and the server (-g):
cmd_args=!-n -q -g -u ntp:ntp
Finally, enable and start NTPD (the commands below
assumes that the root tree is current):
# 66-enable ntpd
# 66-start ntpd
Watch your clock bounce back from the dead!