Meanwhile, heat the milk in a small saucepan, but don't boil it. Melt butter in a pot and add the flour. Cook over low heat for 2 minutes, stirring with a whisk. While whisking, add the hot milk and cook for a minute or two more, until thickened and smooth. Off the heat, add the Gruyere, Cheddar, 1 tablespoon salt, pepper, nutmeg, and ham. Add the cooked pasta and stir well. Pour into a baking dish.