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Whenever you kill the captain and there are still pirates on the boat the note will not spawn on the captain ! 

Are you using a loot plugin? 

I experienced the same issue.  Killed Captain as the last NPC on boat, but no note spawned.

I am NOT using any loot plugins

This worked previously, but it has been a while since anyone completed the event.  I do not know when it stopped working properly

Is the rest of the captain's loot spawning according to the configuration or is it just default npc loot?

There was loot on the captain, just no note with code.  Other pirates also had loot.

Does the captain have his own loot table profile?  It has always been set to the same as the pirates.

Captain profile:
 "lootProfile": "pirate",

This is the same entry for the pirates profile:

Pirate profile:
"lootProfile": "pirate",

I reloaded everything from scratch and did the event myself and a note was on the captain.

Not sure why the note was not there a few times.

Found the issue

When the maximum amount of items in the corpse is exceeded, the loot generator just stops. Since the note is the last item there is a chance that it is skipped

Will fix this with the next update

Changed Status from Pending to Closed

Changed Fixed In to 1.2.2