Boil the cavatappi in water with 1 teaspoon salt for 3 minutes less than the package directs and drain.
Melt the butter in a saucepan, whisk in the flour for 1 minute, then gradually whisk in the warm milk and evaporated milk.
Simmer for 4 minutes until the sauce coats a spoon, remove from the heat, and stir in the mustard, pepper and remaining salt.
Combine the pasta and sauce in a buttered 6-quart crockpot and cook covered on low for 45 minutes.
Stir in both cheeses by handfuls, cover, and cook on low for 30 to 45 minutes until melted and the pasta is tender.