I got to the scene on the boat where the Githyaki board and the ship sinks.
Only it didn`t. No cut scene - I fought them and at one point actually boarded their boat. Nothing happened - the fight just went on and on.
Fortunately my saved game saved me.
Very Funny - Spoiler
It`s 2 years since I played this game, but I remember this happening to me too. Several places, if you played a little more aggresively or "creative" some scripted scenes or dialogues were prohibited from running. The solution to this is to speak to the NPC involved in this quest. Occasionately the game would let him\her repeat his\her last dialogue to "activate" the script again. In your case the solution is to speak to Saemon Haevarian again, I think. Who should appear on the deck during the battle with a blue circle around him.