The way it has been explained to me is this.....
Shipboard credit promotions such as the Disney Visa promotion carry fine print that controls their combinability with certain other credits or discounts. It's all there in general terms in the fine print at the bottom of all of Disney's printed promotional materials.
When I booked with All Seasons, I received a significant price break resulting from a group discount. All Seasons has fought the combinability issue, but it is Disney that controls who gets the credit and who does not. Last year, in the early days of the Visa promotion, the shipboard credit apparently was combinable with the group discount. That is no longer the case. So, most bookings through All Seasons will not qualify for a shipboard credit resulting from the use of Disney Visa. You will still receive the deferred payment provisions and other benefits associated with the Disney Visa.
On my particular booking, the savings through All Seasons far outweighs the lost shipboard credit.
Hope that helps.