Cook pasta in salted water for about 3 minutes less than package directions call for, until al dente.
While the pasta is cooking, in a large pot melt the butter and then add the flour, whisking continuously over low-medium heat for 2-3 minutes to make a roux. Slowly whisk in the milk and bring to a boil.
Reduce heat and simmer, whisking occasionally for 3-4 minutes, or until the sauce is gently bubbling and starting to thicken.
Add the cheese, butternut squash soup, and salt. Whisk until cheese is melted.
Stir in the pasta, transfer to a greased 13 x 9 inch baking dish and bake for 20 minutes, until the cheese is bubbling and the pasta is set. You can also serve this straight off the stove top without baking.