I know how frustrating that can be! I was having similar issues - I had recently uninstalled SH3, cleaned my PC including the registry, re-loaded the game and yet could never successfuly re-load a single saved game. I came across a thread that suggested that the water disturbance and fire damage mods were known to trash saved games a sea for some. I deleted both, and have since successfully (knock on wood) saved and re-loaded 11 patrols in a campaign. I'd suggest you give that a try.
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