I had a similar problem earlier this year when the phone queue times were on the orders of hours. I called into the United Reservations line in Guam at (671) 647-6453 and the agent was unable to apply the certificate. Being that I needed the reservation anyway, I had him go ahead and book it. Later in the day I received an email from the agent letting me know that he figured out how to apply the certificate and attached my new receipt with the discounted price. I was billed the correct amount.

So maybe give the guys in Guam a call, they were able to figure it out for me without any hold time