To make the crust, combine the Nutter Butters and melted butter in the bowl of a food processor or blender and pulse until you have fine crumbs. Alternately. crush the cookies in a sealed baggie with a rolling pin and then mix with the butter.
Press the crust into the bottom of a greased 9x13 pan.
To make the cheesecake, preheat oven to 325 degrees.
Beat together the cream cheese, peanut butter, sugar, and flour until light and smooth and creamy. Beat in the eggs one at a time. Stir in the milk.
Pour batter onto the prepared crust.
Place the 12 Reese's peanut butter cups in the batter, lined up so that there will be one cup in each piece of cheesecake when cut, and gently press them in to cover them in the batter.
Bake for 10 minutes at 325 degrees.
Reduce heat to 260 and bake for 40 minutes or until just the center is slightly jiggly.
Let cool on the counter top for 30 minutes before placing in the refrigerator to cool for another 4 hours.
To top the cheesecake, melt the chocolate chips and shortening together in a microwave safe bowl on low heat. Alternately, melt in a double broiler.
Place the melted chocolate in a piping bag (or baggie with the tip cut off) and pipe on the melted chocolate.
You can also drizzle it on with a spoon, if preferred.
When serving, cut the bars so that each piece has a peanut butter cup in the center.