Preheat oven to 375°.
Melt Butter in small saucepan over medium-high heat. Add Pancetta, cook 1 minute. Add Shallots and Garlic; cook 2 minutes stirring constantly. Add 4 tablespoons flour to pan; cook 2 minutes stirring constantly with whisk. Stir in thyme. Gradually add Milk, stirring constantly with whisk; cook over medium heat until slightly thick (about 3 minutes). Stir in Parmigiano-Reggiano; cook 3 minutes or until cheese melts. Stir in salt and pepper. Remove from heat.
Cook Baking Potato in boiling water 4 minutes or until almost tender; remove with a slotted spoon.
Cook Sweet Potato in boiling water 4 minutes or until almost tender; remove with a slotted spoon.
Cook butternut squash in boiling water 4 minutes or until almost tender; drain.
Sprinkle vegetables evenly with remaining flour. Arrange potatoes and squash in alternating layers in a broiler-safe 11x7 inch baking dish coated with cooking spray; spoon sauce over potato mixture. Top with Gruyere. Bake at 375° for 40 minutes.
Preheat broiler. Broil 3 minutes or until golden.
Let stand 10 minutes.