Found a working fix to this bug. Somehow (perhaps due to the aforementioned duplicating boff stations) the names of the outfits assigned to each of my boffs were all the same (accounthandle_charactername), and upon seeing this I figured that perhaps the character selection screen simply queries the outfit names rather than some actual bridge officer database entry. So I gave all the outfits unique names, i.e. the name of the Boff, and this fixed the display bug completely. No more cloned boffs, and the ship appears properly.
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AHA! That's it. (lightbulb!) And that makes perfect sense.
Thank you for posting this. This bug was driving me nuts, but it's sorted now.