Temperatures over about 150 F break down the protein bonds in the cheese allowing too much of its moisture to escape. Bring your soup to a low simmer and gently toss in a small handful of cheese at a time. Whisk or stir the soup until each handful of cheese is thoroughly melted and incorporated before adding the next.
This can happen if the temperature gets too high. Basically the proteins in the cheese tighten up and squeeze out the fat. You end up with a grainy, curdled consistency.