Position the rack in the center of the oven and preheat the oven to 400°F
To prepare the muffin pans, spray the holes and the rims around them with the nonstick spray or line the holes with the paper muffin cups. If using silicone pans, spray as directed, and then set them on a cookie sheet.
Whisk the milk and malted milk powder in a small bowl until well mixed and the powder has dissolved. Let stand at room temperature for 15 minutes.
Meanwhile, whisk the flour, baking soda, baking powder and salt in a medium bowl until well mixed. Set aside.
Place the chocolate and butter in the top of a double boiler set over simmering water. If you don't have a double boiler, place them in a bowl the fits snugly over a small pot of simmering water. Stir constantly until half the butter and chocolate mixture is melted. Remove the top of the double boiler or the bowl from the pot; then continue stirring, away from the heat, until the butter and chocolate are completely smooth. Cool for 5 minutes.
In a large bowl, whisk the eggs until lightly beaten, then pour in the sugar and continue whisking until the mixture is thick and pale yellow, about 3 minutes. Stir in the the vanilla, then the prepared malted milk mixture. Pour in the cooled chocolate mixture in a slow, steady stream, whisking all the while. Finally, using a wooden spoon, stir in the flour mixture, just until moistened.
Fill the prepared pans three quarters full. Use additional greased pans or small, oven-safe, greased ramekins for any leftover batter. Or save for a second baking. Bake for 20 minutes, or until the muffins have cracked, rounded tops, and a toothpick inserted in the center of a muffin comes out clean.
Set the pan on a wire rack to cool for 10 minutes. Gently rock each muffin back and forth to release it. Remove them from the pan and let cool on the rack for 5 more minutes. (If storing or freezing, cool completely) Seal in an airtight container or freezer proof bags. Muffins will stay fresh up to 24 hours at room temperature or up to 2 months in the freezer.