I bought Custom CSS at the end of last week, and it is not available to me now.
I had one blog, added another, and then deleted the original because I wanted to change the address.
For example, I had matthewscott84.wordpress.com, added Custom CSS upgrade. I then added bexleyblog.wordpress.com to my account, and deleted matthewscott84.
I'm guessing you have to buy Custom CSS for each blog in your account?