1. Preheat oven to 350 degrees F. Coat a 9"x13" baking dish with cooking spray.
2. Bring a large pot of water to a boil. Cook noodles according to package instructions.
3. Melt butter in a large, heavy-bottomed pan oven over medium heat. Add leeks and cook until softened (5-6 minutes). Stir flour into leeks and cook until nutty (1-2 minutes).
4. Whisk in milk in a slow stream and cook, whisking constantly, until thick and bubbling (8-10 minutes). Whisk in thyme, salt, nutmeg, and pepper. Remove from the heat.
5. Grate the butternut squash in a food processor.
6. Assemble lasagna in the prepared baking dish by layering noodles, sauce, squash, and cheese three times.
7. Cover with foil and bake for 50 minutes. Uncover and bake until bubbling and lightly browned (30-45 minutes). Let stand 10 minutes before serving and serve topped with pine nuts.