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Well, that might give me a few more thoughts. Are we definitely talking about flagships, meaning only ships that have a checkered flag flying over the ship itself (black & white check for EITC and red & white check for Navy)?
I ask because I don't currently know of any ghost flagships, although I gather they were in one or more of the beta versions of the game.
Alternatively, are you also having issues with ships that do have flags flying over them, but that sink before you have a chance to grapple/board them? That seems to be a fairly common issue for people; I've definitely been frustrated by it, since it doesn't give any plunder when it happens. This seems to be a bug to me, but it also does seem to happen when I put a very strong attack on a ship that doesn't have many hull points left. The rep usually suffers too, since I typically board a slightly lower level vessel than I look for when I'm just sinking them.
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