This has happened to me twice, the last time yesterday. I wanted to by a Y fare for the Automatic upgrade. I could do the Y-up fare without putting in the ONEPASS code. Then, the screen would come up saying I could save 5% with my MC. When I hit that I got a U fare, non refunable and non upgradeable even though the elite upgrade was noted.

Tech support will make the booking and then deduct the 5% for using the MC. They had to do all that and then forced the upgrade. Its all paid for and is showing in my flight records. I did the seat assignments today.

Its annoying though that you have to go through this.