Combine 2 cups whole wheat flour, undissolved yeast and salt in a large mixer bowl. Add honey, molasses, butter and water; beat for 2 minutes. Add 1 cup whole wheat flour, pumpkin seeds, millet, sunflower seeds and flax seeds. Add remaining whole wheat flour until soft dough forms. Knead on lightly floured surface for 5 to 6 minutes. Cover and let rest 10 minutes.
Grease two 8-1/2 x 4-1/2-inch loaf pans. Punch dough down; divide in half. Roll dough to 12 x 8-inch rectangle. Beginning at short end, roll up tightly as for jelly roll. Pinch seam and ends to seal. Place, seam side down in greased loaf pan. Repeat with second portion of dough. Cover and let rise in a warm draft-free place until almost doubled in bulk, about 1 hour. Bake in preheated 350°F oven for 35 to 45 minutes.