Preheat the oven to 350 F. Cook pasta according to package directions. Drain, and place into a large greased baking dish.
Sprinkle with flour, and top with sliced butter. Sprinkle with both cheddar and pepper jack cheese. Pour milk evenly over the pasta. Cover with foil, and bake for 30 minutes. Remove the foil, and bake uncovered for another 10-15 minutes.