I guess it's possible that the clock was way off to begin with and just hasn't been able to sync with a time server yet.
Usually NTP protocol don't do big jumps in time. It has some limit to the automatic time change. If the time shift is greater than XXX seconds / minutes, it will not update.
Have you tried to config the clock manually to the closest as possible and then asked pfsense to then, sincronize ?
Also, sometimes time settings is not change on the fly on some process. Sometimes it is necessary to restart the service. If it is something related to kernel, usually a reboot will make the time to be correct (if the hardware clock is correct at boot time).
Regards from Rio de Janeiro.