Amazon sells a legitimate CD from the original releasing company.
I don't know what the other stores sell, but there are Taiwanese copies that many stores offer that are direct copies of packaging and the disc. Like all Taiwanese releases, they are only legal in Taiwan, but many places import them anyway because they are much less to purchase and resell.
Have you tried looking at http://www.cdjapan.co.jp ? In a group purchase, they can frequently be less expensive because you can pay shipping for a group rather than "per CD" if you bought them piecemeal + markup from Amazon.