Preheat the oven to 375 degrees and line 2 muffin pans with cupcake liners.
In a bowl, sift together the flour, baking powder, baking soda, cinnamon, nutmeg and salt. In a mixing bowl, beat the eggs at medium speed until blended. Gradually beat in the granulated sugar and the dark brown sugar. Add the vanilla, vegetable oil and orange juice and mix until combined and smooth. On low speed mix in one-third of the flour mixture. Scrape down the sides as necessary. Continue to add the flour mixture in thirds until just smooth. Fold in the grated carrots, walnuts and chocolate morsels. Fill the muffin cups about two-thirds full and bake 18 to 20 minutes or until a toothpick inserted in the center comes out clean. Cool on a wire rack for 15 to 20 minutes and remove from muffin tins. Frost with Cream Cheese Frosting.