It took 3 requests over a month & a 1/2 to get my confirmations from Disney. I usually get these within a week of making the reservation and send a check as payment. When I called the first time, I was told that they would send one out, but unless I paid by credit card that day, the reservation would have been cancelled the following day. Since I had been able to get the AP rate at the CBR & WL for my stay, I did not want to lose it and was forced to grab my credit card while I was on the phone with CRO and pay the deposit. I waited another 2 weeks and called again to say I still had not received my confirmations. Waited another 2 weeks and called for a third time for the confirmations and finally received them a week later. Both confirmations had the deposit applied and I noticed on my credit card bill, that the charges were made the day I originally paid. When I called to check about making a change to my CBR ressie to the WL, the woman first was unable to find it, and when she did, she had said that it was being cancelled due to non-payment. I told her that I had finally received my confirmations from Disney and that the payments had been charged to my credit card several weeks prior. After looking again, she stated that "oh yeah, I do see the payment." Once I picked myself up off the floor, I finished with her and called back to speak to another CM. He confirmed both reservations were fine and that the payments had been credited.
I don't know what is happening down there, but it's making me a little concerned. Whenever I call, I get either CRO or WDWTC and at times am not getting the same information. Whether you pay by CC or by check, I would call and confirm the payment. Better safe than sorry.