Preheat oven to 350 degrees F. Line twenty-four 2-1/2-inch muffin cups with paper bake cups; set aside. In a medium bowl stir together flour, graham cracker crumbs, and baking powder; set aside.
In a very large mixing bowl beat peanut butter and shortening with an electric mixer on medium speed until combined. Gradually add sugar, beating on medium speed until well combined. Beat in eggs and vanilla. Alternately add flour mixture and milk to peanut butter mixture, beating on low speed after each addition just until combined.
Spoon a rounded tablespoon batter into each prepared muffin cup. Unwrap peanut butter cups and place 1 in each muffin cup on top of the batter. Spoon remaining batter into muffin cups to cover peanut butter cups. Bake in the preheated oven about 18 minutes or until a wooden toothpick inserted near edges comes out clean (cupcakes may have a slight indentation). Cool cupcakes in muffin cups on wire racks for 5 minutes. Remove cupcakes from muffin cups; cool thoroughly on wire racks. Spoon a small amount of jam on top of each cupcake. Makes 24 cupcakes.