In a large saucepan, combine the first five ingredients. Bring to a boil. Reduce heat; cover and simmer for 10 minutes or until vegetables are tender. Add 3 cups milk, bouillon, salt, and pepper.
In a small bowl, combine flour and remaining milk until smooth; gradually stir into soup. Bring to a boil; cook and stir for 2 minutes or until thickened. Remove from the heat; stir in cheese until melted.