The weather model for SHIII is broken. The weather tends to get "stuck", usually with high wind, storm, rain, etc..
This is in the stock program and is un-moddable. I believe the latest version of GWX makes the weather a little more random, but nothing is going to be able to TOTALLY fix the problem.
We HAVE discovered a bit of a workaround. We noticed that the weather tends to change roughly every three days of game time. Saving the game, and then reloading it, resets this "timer". So, if say, you're sailing and the weather is perfect with no wind, you save the game when you're out there for two days, and then you exit, and reload your saved game, the timer will reset, giving you another three days of game time of the same weather you had when you saved. This is by no means a 100% as the weather timer DOES vary some for when it changes the weather. Especially the closer you are toward the equator where it changes the weather more frequently.
Hope this helps. Maybe some others have some other suggestions as well.
Also, if you don't know about it, ALWAYS save while surfaced. There is a major bug that will cause you to plunge to the bottom of the ocean when you restart if you save while under water. Also, if you're using the GWX mod, don't save anywhere near a base as it will cause all the ships in the base to crash and burn when you restart.
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