I tried to use SWUs recently about 6-8 hours after choosing them. They showed up in my account right after I chose them and I even got the email with the cert numbers, but 6-8 hours later the SMS rep was not able to see the certs, even when I gave her the number.

If the rep insisted that it would not get you any higher in the queue, he likely coded it wrong or (unlikely) everybody ahead of you is using upgrade instruments. He is absolutely 100% wrong that the only way to get an upgrade is the complimentary Medallion upgrades.