I've noticed the same thing happening since Hotfix 3. However, mine is tied to being unable to load any save files made since Hotfix 3 as well. The game crashes when I try to load a save. Sometimes that crash also resets all settings - including presenting all the "first run" popups such as the nudity preference, cross-save preference, etc. Not sure if they're related, but the one common denominator seems to be Hotfix 3.
