Just a shot in the dark... SH3 Commander has a toggleable setting under SH3 Options titled "Simulate a Realistic Career Length". If you have that checked it will 'retire' your Captain at a somewhat randomized time (not sure how it decides the date.)
I have never used that SH3 Commander feature so I don't know if this is how it would behave in game, but it is the first thing that popped into mind.
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