I am playing full bad ass pirate mode with Charles (rating with all nations are negative except pirates). At my very first stop at Santiago on Cuba (after escaping from Havana in that small boat), I was attacked by the fort. However I was able to dock and go into the town and do the quests. Ever since then, whenever I showed up near the fort with any flags (friendly to Spain or not), I get attacked. And interestingly, I can still dock and go to world map view without problem. I changed several ships and flew Spanish color and still get fired upon. This ONLY happens in Santiago. Other Spanish ports are fine (even Havana, which is on the same island as Santiago). One time I approached Havana under pirate flag and fired upon. I got away, changed the flag to Spain and came back, then the fort no longer fires at me. I remember there used to be a bug like this and it was fixed. But the same bug seems to have come back.