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I have a similar issue however mine has a much more irritating end result. My captian mission cleared itself with the patch but my admiral one is and has been grayed out saying i was ineligeible to get it when i received it. This has resulted in me not being able to purchase ANY ship even with credits for any rank, it wont work at all. I have put in multiple tickets for this issue and gotten no satisfactory results from them. I cannot get my admiral ship, I cannot buy a ship, I am pretty sure I am being shorted 2 officer slots as they are present but grayed out. I cant even guess what else is missing or otherwise screwed up.
Kind of sounds like the issue I had but if it is try discharging a ship you don't need and then buying a new ship.
I also had the same thing as OP that I got the Admiral mission again after promo capt cleared. As others had said after I leveled to Admiral before capt promo was fixed and got the admiral promo, then again after the bug was fixed.