In a large saucepan, cook the cauliflower, broccoli, onion and carrot in butter until vegetables are crisp-tender, about 5 minutes. Stir in 1-1/4 cups milk, bouillon, salt and pepper. Bring to a boil. Reduce heat; simmer, uncovered, until vegetables are tender, about 5 minutes, stirring occasionally.
Combine the flour and remaining 1/4 cup milk until smooth; add to saucepan. Bring to a boil; cook and stir until thickened, 1-2 minutes. Reduce heat; add cheese and stir until melted. Serve immediately.