In your story I can see no obvious errors, except maybe:
a)
The modding of your VIIC/41 must be TWOS compatible, not every mod is compatible, so this could be the problem.
b)
If you save in port that's always ok, don't use autosaves. But the first time you start a main campaign chapter , you must save in bunker, quit to main menu and reload the save, or you will precisely have the trouble you mention, so I strongly guess it's this one.
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