First and foremost, don't let Steam install games to Program Files (x86), that's a bad place, Windows doesn't like anything messing with the Program Files folders, so I would strongly recommend changing the Steam install directory if you have not already done so. Aside from this, I can not speak from personal experience if Steam could be the culprit, since I had no issues whatsoever when modifying my own install through Steam.
Secondly, since you mentioned ending patrols at sea, in my experience with GWX this can cause some really odd behavior on subsequent patrols (I've experienced CTDs, broken AI, ships not loading properly, and some other assorted silliness), so I would highly recommend cruising back to base and docking when within 25km.
Thirdly, pick up Commander, it is the best thing to happen to SH3 since GWX.
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The only sound that still scares me to this day...
The silence when the pinging stops.
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