Ok. As soon as you moved the deck gun to the stern you needed to go into the crew management screen and manually move the crew into/out of the deck gun slots. THis should keep them intact allowing the AI to fire the gun. If not, I don't know what is happening. This works quite well for me. Now that you have this problem, you will have to wait until you start a new campaign. I don't believe it is fixable after it has already happened.
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"You know, you might get surrounded." "We're paratroopers, Lieutenant. We're supposed to be surrounded." --Band of Brothers
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