Heat butter in small saucepan over medium heat. Add onion, if using; cook and stir 5 minutes or until tender. Add flour. Cook over medium heat 1 minute, stirring constantly. Stir in milk and heat to a boil, stirring constantly. Continue stirring and cook for an additional 1 minute or until thickened.
Process half of corn in food processor or blender until coarsely chopped. Combine milk mixture, processed and whole corn, salt, dried thyme, pepper and nutmeg in slow cooker.
Cover and cook on low for 3½ to 4 hours or until mixture is bubbly around the edge.
Add ½ cup shredded Cheddar cheese and 2 tablespoons Parmesan cheese before serving; stir until cheeses are melted.