I had a similar problem a few weeks ago. For some reason when I had the GWX skins mod installed it just made my computer slow. Removing it made it run faster. There is no real reason why it would have done that but it was the only thing that I removed and it fixed it.
My advice is to remove all extras and just try out GWX as it comes fresh after the installer finishes. If that doesn't help try going back to stock patched. If its still slow at stock patched then its coincidental to GWX. SOMETHING is doing it and you might just have to screw around with the set up to find it.
If you use SH3 Commander try launching without it. If you have the 16km mod bring it down to 8km. If you have a new boat skin remove it. Be creative. Computers are really freaking stupid and sometimes the problems defy reasonable logic.
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