In a large saucepan, heat the olive oil over medium heat. Add the onions and jalapeños and cook until soft, about 5 minutes. Add the garlic and continue cooking 1 more minute. Stir in the mustard powder and flour and season with salt and pepper. Stir for 1 minute.
Add the milk and bring to a boil, whisking constantly. Boil for 1 minute and turn off heat. Stir in 1 1/2 cups of the Colby jack and all of the cream cheese. Add the cooked pasta and stir until well coated. Transfer to a casserole dish.
Top with breadcrumbs and remaining cheese and bake for 30-35 minutes until top is browned and cheese is bubbly. Allow to stand for 5 minutes before serving.