In a medium saucepan over medium-low heat, heat the butter until it melts, then continue to cook until it becomes a bit crackly and fragrant, about 15-20 minutes. Remove from stove to cool.
Meanwhile, in a medium bowl, whisk together the flours, baking powder, baking soda, salt, and spices. In a large bowl, whisk together the sugar and eggs, then add the vanilla and milk. Stir in the butter.
Pour the wet ingredients into the dry and stir until well combined. Let batter rest for about 15 minutes.
While batter is resting, heat oven to 375 F. Prepare a 12-cup muffin tin with liners.
Bake the muffins for about 20-25 minutes, until a skewer inserted comes out clean. Remove from oven and place tin on a rack; cool for 5 minutes, then turn muffins out to cool completely. Muffins will keep in an air-tight container for 3 days.