Preheat oven to 375°. On the stovetop, melt butter in a saucepan; remove from heat and stir in flour, salt, and pepper until smooth. Gradually stir in milk. Bring to a boil and stir. Reduce heat and simmer for one minute.
Remove from heat; stir in 1 1/2 cups Cheddar cheese and all of the jalapeño cheese. Pour over macaroni; stir thoroughly. Pour mixture into a 4-quart casserole dish. Sprinkle remaining cheese on top. Bake for 15 minutes; uncover and bake for an additional 10 minutes.