Melt the butter in a large, deep stockpot or Dutch oven over medium high heat. Add the onion, carrots, and jalapenos and sauté until just beginning to soften, about 5 minutes. Add the garlic, salt, and cayenne pepper and cook until the garlic is fragrant, about 30 seconds. Sprinkle the flour over the top of the vegetables, then cook 1 additional minute until lightly golden. Slowly stir in the milk and cook until the mixture thickens, about 2 minutes, stirring constantly.