I will tell you that a properly setup system should automatically start and run properly. So something is "unique" about your setup. I don't know what it would be, but you might want to look in your logs and see if the server is trying and failing or what. I know AD and CIFS are tightly integrated, so if AD is failing to start it probably is preventing CIFS for starting as well.
If you can't figure it out you might want to throw a debug file up here and see if someone else can figure it out. ;)
I will tell you that more often than not, when I've had to troubleshoot AD issues, it's more often than not either a misconfiguration by the admin on the FreeNAS/AD settings or the actual domain itself is not healthy and has major problems. I've had quite a few users that practically took offense to me even investigating his AD settings, and I've had users that were humbled to find that their domain was not as in tip-top shape as they thought.