Melt the butter in a large stockpot over moderate heat. Add the onion and saute until soft, about 5 minutes. Add the tomato, garlic, jalapeno and salt and cook 1 to 2 minutes longer. Add the squash and stock and simmer, covered, for about 20 minutes, or until the squash is falling apart and soup is thickened slightly. Puree soup with an immersion blender, or use a blender and return soup to a clean pan. Add the milk and heat gently. Stir in the cheese and adjust the seasonings.