Deep Six, were you in port at the end of the calendar year, and your next patrol went to sea after January 1st? There is a bug, that I've not seen mentioned elsewhere, where SH3 ignores your torpedo choices if the calendar changes year between your refit and set sail date. Each year has a default loadout, and for whatever reason SH3 will reset your choices if the new year occurs during your refit.
Only way I know of to avoid it is either to
-- add days in base to reach January 1st before launching the patrol (you can change your flak gun a few times to add days, doesn't cost renown and each change adds two days
-- shorten your days in base to set sail while still in December.
If you are not at the new year, kindly disregard
