Did you clean out all old traces of SH3 when you re-installed?
Personally I would avoid Program Files (with or without x86) to prevent Windows messing up the install of GWX.
Also, it can sometimes help when you shut down the game after you finnished the last patrol. So the game completely stores the results. Then restart the game, with SH3 Commander if you have it, to start the next patrol.
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