This is very frustrating. From what I understand of the publishing industry, the Kindle sales are not counted towards the main NYT best-seller list, so all the focus on the initial launch is around selling the physical copy. This is said to be done to prevent gamification and manipulation, but this still goes on with the hard copies also, where would-be best-selling authors often pay third-party companies to buy a lot of copies of their books from certain bookstores.

Source: A friend of mine who has been trying to get onto the NYT best seller list.