gdjoslin, Please don't take offense to what I am about to say, it isn't directed to you. It is a comment in general.
Travel Agent commission is often misunderstood by those that don't work in the industry. Which is why I don't think it should be brought up on public forums. For the sake of this conversation though, this TA will not make any more commission whether the cabin is kept as a quad or there are two triples. The 3rd and 4th person rate are the same.
IF this TA made a mistake, (I say IF, because none of us know what transpired in the request for the extra person to be added. It sounds like the request was made at a later date then the original booking. Was the request made in person, via email, or by phone? We don't know where the miscommunication came in). The TA may be reluctant to make the change now, because it's possible there could be costs involved in making changes since final payment has been made.
Regardless of how this mistake happened, you need to get this taken care of now for the reason mentioned in my earlier post. New security measures require the manifest 1hr prior to the ship sailing. You don't need any problems on the sail date. If the cruise starts out on sour grapes it will spiral into the whole cruise. If you don't want to deal with this TA in the future fine, but you need to stand up and take care of this now.
As for the double payment; we don't know how long ago it was noticed and requested to be charged back. Charge backs can take a couple of billing cycles depending on the card cut off date.