Quick update. I called Hotels.com just now to get my Disney confirmation # and not just their own. She was able to give me another number right away. Tried it on My Disney Experience, didn't work. So I called Disney, gave the CM both numbers given to me by Hotels.com and neither brought it up. However, she was able to find my booking through my phone number, booking dates and last name. All the details were correct, except the address she had for me was actually Hotels.com address so she changed that.
So I booked CSR about 5 days ago through Hotels.com (not a better rate than Disney at the moment, but I had the option to pay Paypal which I prefer) We don't travel to October and Disney already has our reservation, which is now in my own name, not Hotels.com. I am just making note of this because I saw another thread where a poster said that through third party sites Disney did not receive the reservation until days before making DME and other reservations difficult without a Disney confirmation #. Not the case here.