Cook ground beef in a large skillet until no longer pink, stirring to crumble. Drain and set aside.
Sauté jalapeno pepper and 1/3 cup of the chopped onion in hot oil until tender. Add tomato sauce and next 5 ingredients; stir well. Bring to a boil; reduce heat and simmer for 15 minutes, stirring a few times.
Combine flour with water; stir into the tomato mixture. Cook over medium heat, stirring constantly, for about 1 minute, or until thickened.
Combine 3 cups of the shredded cheese with remaining onion; set aside remaining 1 cup of cheese for topping.
Using tongs, dip a tortilla into the hot tomato mixture; sprinkle about 2 tablespoons of ground beef and 1/4 cup of cheese mixture down the center of a tortilla. Roll up jelly roll style and place, seam side down, in a lightly greased 13x9x2-inch baking dish. Repeat with remaining tortillas. Spoon remaining tomato sauce over tortilla rolls; cover pan tightly and bake at 350° for 25 minutes. Uncover and sprinkle with reserved 1 cup cheese and continue to bake beef enchilada casserole, uncovered, for 5 minutes longer, or until cheese melts.
Calories per serving: 700