I too have a strong reaction when I eat food with high levels of msg, but I have never noticed any reaction due to nutritional yeast.
However, in a blood analysis I had done, it was revealed that I had a high level of uric acid. I am a vegan, so this could be from the large amounts of legumes I consume (lentils, beans, peanuts, etc.) but now I worry that the nutritional yeast I sprinkle on every salad, on pizza and on popcorn could be an added cause.
I'm curious what prevents the body from properly digesting or excreting uric acid.