Preheat oven to 350°F.
Meanwhile, sift together the flour, baking powder, baking soda, and cinnamon in a medium bowl; set aside.
In a large bowl, cream together the margarine, sugar and molasses with a hand mixer for 2-3 minutes, ‘til lighter in color. Beat in flaxseed mixture, soy yogurt, salt and vanilla.
With mixer on low speed, incorporate half of the flour mixture, followed by the soy milk mixture; finish with the remainder of the flour. Continue beating the batter 2 minutes to develop the gluten. Stir in the cooled pecans.
Fill cupcake papers 2/3 full. Place pans in oven and bake cupcakes for 22 to 24 minutes or until toothpick inserted in center comes out clean. Remove from oven and let cool in pan 5 minutes before transferring them to a cooling rack.
Let cupcakes cool completely before frosting OR leave cupcakes unfrosted and serve with vanilla ice cream or dairy-free ice cream alternative.
The centers of the cupcakes will sink slightly as they cool, creating a gooey interior.