Hi Gentlemen,
It is indeed an age-old Stock SH3 bug that no-one has been able to fix yet.
My solution generally in general has always been to make-do on the first patrol, and maybe return to base sooner than I might have on following patrols.
You can technically sail a patrol for a little over 24 hours, and go out at least 51km away from base to get the bug out of the way, but I always feel guilty about that when I do.... unless I am testing something. I usually just eat that bug and smile.... because.... I'm on a boat!
(WARNING: NSFW Explicit.... but hilarious!)

I hope this was useful as a morale booster to someone somehow.