The passes sold by railway companies (special-issue tickets) have conditions on who can purchase them, such as their sale being limited to short-stay visitors to Japan from other countries (as with the Japan Rail Pass). So even if you paid for a pass through an online service, if you do not meet the qualifications for use of the pass, they will not issue the pass at the ticket window and you will not be able to receive it. Confirm the reason why they will not issue it.