I think the bug's still there. I'm playing on STEAM version 1.2.0.0017. After I delivered the 'cargo' to Sayuka, dived down to Cignath Mor where I deactivated the machiene and killed the Kraken the quest didn't update at all. I also can't talk to anyone including Fleet Master Okaya they all either complain about something personal or tell me to go away. I have positive 1 reputation with the Deadfire Company too.