I played through as much as I could actively find last night and forgot to post about it when it happened, but when I went to the docks to help the eel and had the encounter with the black cobra (that venom has very interesting side effects. lol), he stayed on the screen long after I left the docks. He didn't disappear until I entered the Tavern after. I haven't played it since last night so I haven't tried to reproduce the bug but I felt I should at least mention it.
Edit: Now that I think about it, there was another odd thing that happened. When I went to see Father Gustav at the chapel, after he mused about someone taking care of the pirate, the entire 'conversation' abruptly ended and I was back in the main room of the chapel again instead of sitting with Father Gustav.