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In the 1337 scenario, if you look at france, they own normandy on the character selection screen. Once you start playing, normandy instantly gets transferred to Navarra.
Without even looking at the files, I bet what's happened is that the counties in Normandy are owned by Phillipe III of Navarre, but still have France scripted as their liege. The game is not designed to multiple liege relationships when a character holds titles in more than one kingdom but the engine is quite robust so when you start it sorts it all out. The in-game state is (presumably) the correct one.