I may be able to shed some light on this, because I did a lot of run-throughs of this quest to test out many variables, including the missing officer. I'm running Build 13 Final.
When I am in the tavern, after talking to Tobias, an officer gets bumped. The one that gets bumped is the last one in your F2 manager under the Passengers tab, at the top (last one on the right). It has no relationship to the arrangement of how they are assigned in the bottom four squares. The one that gets bumped, therefore, is the last one you hired, usually. The way to prevent "loosing" someone here is to hire a placeholder officer when you enter the tavern. The placeholder will return your ship to Redmond and when you eventually get to Redmond you won't owe him anything because he technically hasn't been with you more than zero days.
When you leave the tavern, any officers you have assigned to protect you on the run to the shipyard will run with you and Tobias. Once you get to the shipyard, however, they are removed.
Another thing I was trying to work through is getting to keep both Tobias and Rabel Yverneav. I want to keep them because they are Comrade-In-Arms instead of salaried crew and therefore (theoretically) don't cost a monthly fee. The second I leave the harbor, my ship I'm escaping in, a corvette, is attacked by the port. There are also two class 2 ships and one class one Battleship in the port that are attacking me. So I board the Warship and swap it for the now-battered corvette and escape.
I then went to Isla Muella, refitted the ship and set sail again, under my character flag.
I saw French ships attacking English ships and swooped in. I made Tobias and Rabel Yverneav captains of their own ships, and I put my gunner on the fourth captured ship. Then I returned to Oxbay with the 4 ships.
The governor takes whatever ship you are on (your main character) and gives you back your original ship. Any escorts you have stay escorts. The captain who sailed your ship back goes into your personnel manager (the F2 Passengers tab), but is obviously not made an officer. If you have Tobias and Rabel Yverneav on their own ships, the governor will not remove them from your employ.
When all was said and done, this was my F2:
(first time posting a pic here, lets see if it works)(Pieter: Do I have to leave this image on my web site or has this Forum "got it")
<img src="http://www.ils.unc.edu/~stmartin/Victoria1.JPG" border="0" class="linked-image" />
Later, you have the option to get a Gunner. He is a Comrade-In-Arms gunner (suspiciously named Attwood) and not a salaried employee (I haven't verified this and he asks for 1500 a month but it doesn't show that I'm paying him when I look at his character profile). Unfortunately he's not a "real" gunner in that he doesn't restock your ammo when you board, and he follows you into the captain's cabin instead of hanging out on the deck like most Gunners.
Another interesting thing to note: Rys Bloom and salaried officers go into a dialogue option when you converse with them about crew, buildings, etc. Attwood the Gunner, Tobias, and Rabel Yverneav say something specific based on their mission or what-not, but conversing with them is basically useless. I'm hoping these guys are free because they are Comrade-In-Arms. If not, I'll post it under my previous thread on that subject.
Henry Avery