UPDATE
Finally heard back from Executive Office today regarding my experience @ Boardwalk Resort and using gift cards upon check-in.
CM who assisted me was incorrect, as Disney continues to have the same payment policy: whatever method you pay, the refund will be applied in this manner. The CM supervisor whom I spoke with today has sent a memo to all resorts, as well spoken to the the team lead at Boardwalk, so he/she can review the policy will all of their staff.
She said the CM must give you back your gift cards, so that any refund can be applied back to those cards. They will not issue checks or cash refunds whatsoever, if you have used a gift card at check-in, so you must keep them if you think you will be owed a refund.
She said the best way is to apply the gift cards in small amounts, should you be worried about not spending all of the gift card money, or losing your gift card. In that event, you will not be refunded until you can produce the gift card used at check-in.
She apologized for my experience, and said thanks for bringing it to their attention, as it shows that they need to re-train some CMs in this procedure.
Hope this info helps, Tiger