Its a strang problem this I've had it too. I get round it by moving my DG as soon as I start a new career game it usually lets me then. Fleet boats had their DGs repositioned forward very early on anyway so I save myself the hassle by doing it then.
Another thing I do, and don't know if this has any bearing at all, is stop assigning extra crew to man the DG in the first place when in port. Instead I just draw them from the watch crew like SH3.
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