I used to be Delta Medallion and a credit card holder, it was never a problem. They are connected to the airlines reservation system and it comes up as long as your frequent flyer number is connected to the reservation.
One issue I had with American - I tried to show the card on a work reservation that I made before I got the card. They would not honor it. After that though, it worked on my work reservations made with my Corporate Card. On the other hand, I cancelled my card last June. I had made a reservation in February using the card for a personal trip in October. Much to my surprise, they gave me the free luggage and early boarding, I guess because I had the card when I made the reservation.