Dinged just before the servers kicked me out, went to the ceremony and everything, but my Lt.Cmdr skills are still greyed out. Earn more SP?
From what you are describing it makes me think that you haven't spent the points to truly "earn" the rank of Lt Cmdr. Not only do you need enough earned SP, but you need to spend enough SP to unlock the Lt Cmdr skills. That, or you don't have 200 SP to spend on a Lt Cmdr skill.