Lightly grease a 9x9 casserole and preheat the oven to 350F.
Heat the butter in a skillet and cook the squashes, onion, jalepeno about 10 minutes, until softened.
Add the garlic, cumin, chili powder and cayenne and cook a minute. Add salt and black pepper to taste.
Stir in the flour and cook a minute or so, stirring.
Stir in the broth and tomatoes and cook a minute or so, until thickened.
Turn off the heat and stir in the half and half, sour cream and cilantro.
Put the crushed tortilla chips on the bottom of the casserole dish, then pour the squash mixture over them. Top with grated cheese. Bake uncovered about 30 minutes.