I think that the 1.6 patch by H.sie sets some maximum amount for stormy seas (actually the default value is around 3 days, if I remember right). On the other hand, loading a save resets the weather change timer (usually between 20 and 40 hours) randomly from 5 to 90%, so you could really effectively prolong the current weather if you reload a lot.
This all may be completely wrong, it is a long time since I last probed these files, but I am quite sure that what I said is more or less true.
You may be just unlucky, hang in there mate!
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