Bring potato and salted water to cover to a boil in a large saucepan over medium heat; reduce heat, and cook 8 minutes or until tender. Drain and set aside.
Cook bacon in a large skillet until crisp. Remove bacon from skillet. Drain on paper towels, reserving 2 tablespoons drippings in skillet. Crumble bacon, and set aside.
Sauté onion in drippings in skillet over medium-high heat 15 minutes or until tender. Stir in bacon and chives.
Layer a lightly greased 13- x 9-inch baking dish with one-third of potato slices, one-third of onion mixture, and 2/3 cup cheese; sprinkle with 1/3 teaspoon salt and 1/4 teaspoon pepper. Repeat twice.
Melt butter in a heavy saucepan over low heat; whisk in flour until smooth. Cook, whisking constantly, 1 minute. Gradually whisk in milk until smooth. Pour over potato mixture.
Bake at 400° for 35 minutes or until golden. Let stand 10 minutes before serving.