In a medium mixing bowl, stir together flours, ground flaxseed, salt, and baking powder. Make a well in the center of the dry mixture; set aside. In another medium mixing bowl, beat egg yolks slightly. Stir in milk and melted butter. Add egg yolk mixture all at once to the dry mixture; stir until moistened (batter should be lumpy). In a small mixing bowl, beat egg whites until stiff peaks form (tips stand straight). Gently fold beaten egg whites into flour and egg yolk mixture, leaving a few fluffs of egg white; do not over mix. Pour about 3/4 cup batter into grids of preheated, lightly greased waffle iron; close lid quickly and do not open until done. Bake according to manufacturer's directions. When done, lift waffle off grid with fork. Repeat with remaining batter.
Higher protein variation: Add 3/4 cup vegetarian protein powder to dry mixture. Decrease milk to 1 1/2 cups and add 1/2 cup water to wet mixture. Continue with recipe as directed.
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