It's a glitch with POL's Linkshell Community, from what I understand. I am a Captain as well, yet the Linkshell Community site continues to only show First Lieutenant.
Once SE gets their junk together this should update as well.
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I take it there's still no solution to this? I was going to suggest that maybe you could just assign people as captain if it shows they've finished ToAU and have completed all the assaults (which would get them captain), but then I think Assaults are user populated?