Unfortunately we had a similar experience recently. It was a bit later, I think we arrived around 9:30 or 10 on a Saturday. They were out of chowder, bisque, and rolls, as well as who knows what else that we didn't try to order. No one was impressed by the food and then at the end of meal we were told our restaurant.com certificate was not valid.
Fortunately restaurant.com has excellent customer service and exchanged it for us because we weren't planning to go back again to see if next time they will accept the certificate! They also confirmed that there was nothing wrong with the certificate which makes me wonder what went wrong because that was the first time we've ever had an issue redeeming a certificate