Preheat oven to 350 degrees F and line 12-cup muffin pan with cupcake liners.
Melt the butter in a medium saucepan over medium heat. Stir butter occasionally over the heat until the butter is browned. Transfer to a large bowl and let cool for about 5 minutes. Whisk in the sugar, eggs, milk, and vanilla extract.
In another bowl, mix the flours, baking powder, and salt. Add the dry ingredients to the wet ingredients and stir until blended. Mix in the chopped caramel corn.
Divide the batter evenly into the prepared muffin cups (about 2/3 full).
Bake the cupcakes for 18-22 minutes or until a toothpick inserted into the center comes out clean. Cool completely before frosting.
To make the frosting, beat the butter and brown sugar on medium-high speed until light and fluffy. Add the remaining ingredients (except the caramel corn) and mix on low speed to combine. Increase speed and beat frosting until fluffy, for a couple of minutes.
Spread layer of frosting over the top of each cupcake and garnish with the caramel corn, as desired.