This makes no sense. If you booked through Disney, it should link to your MDE account. There shouldn't be any reason that it would take two weeks. I would NOT be satisfied with that answer. I would call back and get a different CM. If they can't solve your problem, ask to speak to their manager and move this up until you find someone to help you.
So you confirm my suspicions. I will try to call again and to solve the problem.
Are you usually able to link the reservation immediately after receiving the invoice and the confirmation number?
Thank you again!