If you're running FreeNAS 8 under VMware, Xen or KVM, then you'll probably want to disable ntpd. To do this you'll need to ssh into your FreeNAS box as root and run the following commands.
mount -uw / vi /conf/base/etc/rc.conf
Change ntpd_enable="YES" to ntpd_enable="NO" and ntpd_sync_on_start="YES" to ntpd_sync_on_start="NO".
Then reboot and you should find that ntpd has been disabled. This should help eliminate any time jitter issues when running ntpd on a virtualised environment.