In a large pot over medium-high heat, cook beef until brown. Drain and return to pot. Stir in onions, bell peppers and jalapenos and cook until tender. Stir in garlic and cook 1 minute more. Season with chili powder, cumin, salt and pepper. Stir in the tomato paste and kidney beans with their liquid.
In a food processor or blender, puree the tomatoes with the chipotle peppers until smooth. Stir into the pot with 3 cups of water.
Combine the remaining 1 cup water with the flour in a jar and shake to combine. Pour into the chili and stir in the vinegar. Simmer about 45 minutes before serving.
