That would be a weird bug (although the nature of bugs is that they do weird things) since the only time the game checks persistent data (ie variables that were not created during the particular game instance in progress) is at the very end of a run.
SPOILERS FOLLOW
Seeing your answer to IlLuco27's question below, though, I suspect it's because you're not prioritizing high protein foods. You can only get on the super-fit arc if you hit the gym regularly and take in a certain amount of protein as well - it's not just how much you eat, but what you eat, that matters. Does it put you on the fat arc if you visit the gym, avoid high-carb / high-sugar food, AND each protein rich (burgers, chicken, eggs) stuff?