During "Vogelstruijs", when you board the ship and the captain spots you, you become hostile to both England and Holland. Here's why:
"Skipper1" always seems to be English by default. If he's English then he's a traitor, helping Spain to attack an English colony, so if anything England should reward you! Holland shouldn't care as he's a smuggler. And anyway, about the first thing Contre Amiral Beauregard says is that nobody must know what you're up to, which you've achieved unless you said the wrong thing to the captain's wife when you burgled his house, so neither England nor Holland should change their relations to you at all. (If you did say the wrong thing to Mrs. Skipper1 and she called the guards then Holland becomes hostile there, which is reasonable; you've been caught red-handed breaking into someone's house in a Dutch town so they now regard you as a criminal.)
So I'd be inclined to remove both "SetActualRMRelation("Skipper1", REL_WAR);" and "if(GetRMRelation(GetMainCharacter(), HOLLAND) > REL_WAR) SetRMRelation(GetMainCharacter(), HOLLAND, REL_WAR);" from this part of the quest.
Code:
case "birdhunt3":
bQuestDisableMapEnter = true;
UpdateRelations();
Group_CreateGroup("Skipper1");
Group_AddCharacter("Skipper1", "Skipper1");
Group_SetGroupCommander("Skipper1", "Skipper1");
Group_SetTaskRunAway("Attack");
Group_LockTask("Skipper1");
Group_SetAddress("Skipper1", "Hispaniola", "Quest_ships", "quest_ship_6");
SetActualRMRelation("Skipper1", REL_WAR);
Sea_LoginGroupNow("Skipper1");
characters[GetCharacterIndex("Skipper")].nosurrender = 2;
SetCharacterRelationBoth(GetCharacterIndex("Skipper1"),GetMainCharacterIndex(),RELATION_ENEMY);
if(GetRMRelation(GetMainCharacter(), HOLLAND) > REL_WAR) SetRMRelation(GetMainCharacter(), HOLLAND, REL_WAR);
So I'd be inclined to remove both "SetActualRMRelation("Skipper1", REL_WAR);" and "if(GetRMRelation(GetMainCharacter(), HOLLAND) > REL_WAR) SetRMRelation(GetMainCharacter(), HOLLAND, REL_WAR);" from this part of the quest.