Does nutritional yeast make you bloated?

Fermentation. It certainly can. Consider that yeast is used to make bread (which rises up from the gas bubbles produced)... and of course beer which has all those bubbles! So if you're consuming yeast - I would expect 'gas' to form in your GI tract and created the bloated symptoms you're feeling. Why not take a break from the yeast and see if it goes away?