1. Preheat the oven to 375˚ and position a rack in the bottom third. Place 2 muffin pans (or enough to make 16 popovers) in the oven to warm.
2. In a small saucepan, warm the milk over medium heat until it is hot (about 125˚) but not boiling. Remove from the heat. In a large bowl, whisk the eggs with the salt and black pepper until smooth. Slowly whisk in the warm milk. Add the flour and whisk until the batter is just combined. (It may be slightly lumpy.)
3. Remove the muffin pans from the oven. Spray the pans generously with nonstick cooking spray. Pour about ⅓ cup of the batter into each of 16 muffin cups. Set a cube of the cheese on top of the batter in each cup.
4. Bake the popovers until puffed and deep golden brown, about 40 minutes (do not open the door or they may collapse). Remove the popovers from the pans, sprinkle with the grated Gruyère and serve immediately.