I think I had something similar happen on more than one occasion but with my memory lately (swear I gotta see a doctor soon), I can't recall for certain. I know that if you set your options in both the Home Port and Main Menu, I think the Home Port settings take precedence. Just to be certain, from now on, save a game immediately out of port, restart the game and double-check your settings. I do this all the time now, and I think
, it's because I encountered a similar issue.