Cook the pasta in a large pot of salted water (a teaspoon of salt per quart), then drain and set aside. Your goal is to boil the pasta until its just barely cooked through, or al dente.
Put the pot back over low heat, add the butter, and melt.
Add the flour and stir for 1 minute, until the mixture bubbles. Raise the heat to medium.
Gradually add the milk, stirring all the time.
Then add the nutmeg and bay leaf and bring to a simmer, stirring constantly, particularly at the edges of the pot to keep the flour from burning. When the sauce simmers it will thicken.
Turn the heat down to low and cook at a bare simmer for 5 to 10 minutes; this cooks away the floury taste.
Remove the pan from the heat. Discard the bay leaf. Stir in the mustard.
Now add the pasta and the cheeses. Put the pan over very low heat and stir to melt the cheese.
Season with 1/4 teaspoon salt and 1/4 teaspoon pepper. Spoon out into a serving bowl, or onto serving plates, and serve immediately.