You have a couple of options. I take it you didnt apply the patch when you were in port? At sea saves are not compatible across patch versions.
Either start over, which isnt something enjoyable - or uninstall and reinstall and patch to 1.1 - finish your patrol and then patch up to 1.2 - that will allow you to load your last IN Port save. Good Luck!
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Good Hunting!
Captain Haplo
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