Preheat the oven to 350°F (175°C) and line a cupcake pan with paper liners.
In a large mixing bowl, sift the cake mix, then add in the instant vanilla pudding mix, flour, dark brown sugar, eggs, sour cream, water, oil, and vanilla extract.
Mix on low speed for 10-15 seconds to incorporate the ingredients, then increase to medium speed and beat for 2 minutes. Pause occasionally to scrape down the sides of the bowl for even mixing.
Carefully fold in the 1¼ cups of chopped, buttered pecans until evenly distributed throughout the batter.
Spoon approximately ¼ cup of batter into each cupcake liner, filling them evenly.
Bake the cupcakes for 15-17 minutes, or until the tops spring back when lightly pressed, and a toothpick inserted into the center comes out clean or with only a few crumbs.
Remove the cupcakes from the pan shortly after baking and place them on a wire rack to cool completely.