Looks like I'm just going to have to trust Delta on this one. Just spoke to yet another agent who confirmed that everything was as it should be. I even had her read the cert # off to me, and it did match up.
With my luck, If I had them remove the cert and reapply, I'd lose on time of request and be left standing at the gate as #1 with zero left.
I haven't requested a complimentary upgrade for the segment (not that a PM on a V would clear ATL-PDX anyway), so if I'm not on the upgrade list at all at T-24, I'll know there's a problem.