Did you save while at sea? If so, it's possible that you saved too close to the convoy, or other ships, that can have an occasional adverse affect on saves. Also, I believe that loading a save too close to AI units can cause them to lose their orders, drive in a straight line, and then sink randomly (I could be wrong, but I swear I read that somewhere).
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The only sound that still scares me to this day...
The silence when the pinging stops. 
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