You could do a disk error check to see if any files got corrupted. (disk defrag doesn't fix anything, it just tidies up the clutter so it can find the files in just one place) Right-click on your drive, select properties, go to the Extra tab, choose the top: error check or whatever Microsoft translated it into. The operating system might complain that this needs to be done after a reboot. Allow it to do so.
I don't know what kind of files are loaded at the very beginning when SH3 starts. If you have absolutely no mods or tweaks done on it you could let the setup perform a repair. But it might require that the game be patched up again afterwards. (if the dvd wasn't 1.4 allready) If you have some mods applied then they will probably be lost. Other than that I have no idea. It's imposible to tell without knowing what file (or setting) he trips over.
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