I had the same thing happen. Completed all in the family before the patch, Tarquin is on the ship. Patch hits, Tarquin does his routine that he starts at the beginning of Act 2 (goes to the beach, ends up at the graveyard). He's still at the graveyard where the only dialogue option is 'end', and Malady acknowledges that he isn't on the ship. No amount of sitting around (left the game running for hours) nor zone changing have fixed this.
How can quest flags be this hard?