In a medium saucepan, melt butter over medium heat. Whisk in the flour, until a smooth paste forms. Cook the flour, whisking often until the flour begins to darken and smell slightly toasted, 2 min.
Add ¼ c of milk. Whisk the mixture until the flour has dissolved and the mixture begins to thicken. Add the remaining milk, ¼ cup at a time, whisking as you add to ensure no clumps of flour remain after each addition. Heat the milk over medium heat until it thickens slightly, 10-12 minutes.
Remove the pan from the heat and let it cool slightly. Add the shredded cheese, ¼ cup at a time, mixing after each addition until the cheese has melted. (If the sauce cools to the point where the cheese isn't melting, return the pan to low heat, just until it begins to melt again.)
Once all the cheese has been incorporated, stir in the jalapenos, if using.
Serve warm.*
Notes
*This sauce can be made ahead and re-heated. Be sure to re-heat the sauce over very low heat, stirring often.