OK, I think I can see what's happening. Danielle is supposed to assign herself as an officer when you meet her in San Juan, and is supposed to be unremovable so you can't unassign her. That should mean she's always around when you need to talk to her for quest purposes.
Somehow she's managed to be unassigned anyway. Some sidequests assign officers to you, but as far as I can tell from your questbook, you haven't done any of those. But you have hired some extra officers, whether from tavern or from street walkers, and when you hire one of those, he goes into a random slot. So my guess is that when you hired an officer, he went into slot 1 and displaced Danielle.
I've an idea about sorting out random officer hiring to attempt to prevent this, as it has the potential to foul up other storylines as well. But for now, try this version of "quests_reaction.c". Download it and put it in "PROGRAM\Storyline\standard\quests". It includes a check, when you go to the lighthouse, to see if Danielle is an officer. If not, it assigns her as one, then puts her on the beach so you can talk to her. That ought to take care of the problem regardless of how Danielle managed to get unassigned. I've tried it using your savegame.
