If I am reading this thread right I think I found a similar problem. While it is nice that ships that can't put crew on them are skipped for crew distribution, it also seems to skip ships after that one (that it should be able to field). I had a Lasher and a Wolf with full crew and 5 people to spare. I captured a Dominator (due to the enemy not having enough crew to field it), and when I put it as my first ship it said "Not Enough Crew". Now, that was expected, but curiously enough my Lasher and Wolf (my only other ships) were also marked as "Not Enough Crew". When I moused over all the ships, no ship had a single crew in them, while I had more than enough crew to field the Wolf and Lasher. If I put the Dominator after the other two ships, they got crew, but when the Dominator was first they did not.
I think I might know what the problem is. I think that even when ships are "skipped", it still reduces the amount of crew in the pool (for the purpose of testing if it can crew them), causing the ship to effectively be crewed anyway.