Sounds like mod soup to me. Some mods have ships that don't exist in stock game. When the recognition manual from the mod comes up with a boat the game doesn't recognize, do you think the game just sensibly ignores it and carries on? NNNNOOOOOOOOOOO! As John Belushi used to say. It crashes.
You could also be loading up a mission or a saved game that contains "forbidden ships" and nothing might be wrong with your installation at all.
I haven't modded the recognition manual, so I can't be more specific than what I've said. There are others who can tell you exactly what is happening and what to do about it.
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