Lightly spoon flours into dry measuring cups; level with a knife. Combine flours, flaxseed, and next 4 ingredients (through salt) in a medium bowl, stirring with a whisk.
Combine milk, butter, and eggs, stirring with a whisk; add milk mixture to flour mixture, stirring until blended. Fold in mashed banana.
Preheat a waffle iron. Coat iron with cooking spray. Spoon about 1/4 cup batter per 4-inch waffle onto hot waffle iron, spreading batter to edges. Cook 3 to 4 minutes or until steaming stops; repeat procedure with remaining batter.