Cook the pasta according to the package directions in a large pot of salted water.
Meanwhile, make a roux. Melt the butter over medium heat in a large nonstick skillet; stir in flour with a wooden spoon until smooth. Cook for one minute.
Gradually stir in cream; bring to a boil. Add the jalapenos to the cream mixture. Cook, stirring constantly until thickened, about 2 minutes.
Reduce heat. Stir in cheese until melted, then stir in the freshly grated nutmeg and cayenne pepper.
Reserve 1 cup of the pasta water. Drain the pasta; add to cheese mixture. Cook and stir for 3 to 4 minutes or until heated through. If the pasta is too tight and gooey, stir in about ¼ cup of the pasta water at a time to get the desired consistency. Serve immediately.
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