In a large saucepan, combine the first five ingredients; cover and cook over medium heat until vegetables are tender, about 5 minutes (do not drain). Combine flour and milk until smooth; gradually add to the vegetable mixture. Bring to a boil; boil for 1-2 minutes, stirring constantly. Remove from the heat.
Stir in cheese; cover and let stand until melted, about 5 minutes. Stir before serving.