This may be related to the other bug I reported (which has been added to the known issues list), where v-sync setting doesn't save properly. Although in that case, the setting
appears to save aright, and it's only the visual tearing that gives away that it hasn't.
In the case of the v-sync bug, setting the game to borderless window then back to fullscreen will fix it until the next time you start up the game. I don't know if it would work for these other settings, but maybe give it a try,
@justinwow.