FWIW -
We've stayed at either Swan or Dolphin I think our last 5 times (memory fades) and I always call the Swan / Dolphin number during normal business hours weekday so I don't get pushed over to the corporate (Starwood, now Marriot) reservation line
I have wondered at times if maybe I was talking to the corporate line anyway, but I always as strike up a conversation aiming at determining if they are familiar with the layout of the hotel, the amenities, restaurants, proximity to Yacht and Beach, Boardwalk, Epcot, etc. Anything that shows they know the grounds etc better than I do.
As soon as I get a "don't know" about anything basic, I say I'll call back.
Now that isn't necessarily a cure for people having trouble linking reservations - but I will say the last trip and this one (using MDE) we had no issue linking at all.
EDIT - we are at the Dolphin this time and last; not sure if that vs Swan makes a difference)