it seems like the captain is stuck in the doorway near the bow of the ship. I went in that room and logged back out then in, and when I went through the doorway, the captain spawned. It seems like if she is stuck like that, you will have to fight her there.
I first noticed this location when I keep logging in and out, and when I pass the other doorway. for some reason I was able to see the captain, but as soon as I leave the doorway she disappears,
Guys - to fix this in the meantime, please log out (or use /camp) in the doorway where the Mob is meant to spawn. If you kill her as you log in, you can progress.