Undo the mods in JSGME and try again to see if the game works as it should. If not, reinstall the game, as it would seem your game install is corrupted now.
Try to have the Steam game library in a path that is not anywhere inside c:\Program Files (whatever). This path makes Windows prevent making changes to the files. Try to get it in something like c:\Games\Steamlibrary\steamapp\common\SilentHunter III
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