The AMEX certificate is deceiving, as the website will show an upgrade request. The certificate is not upgrade-eligible and all other systems will (properly) reject such an upgrade request...
Similar experience to yours on JFK-PHX-ATL-LGA in early December. Site showed upgrade requested, and no-go at any of the gates.
edit: Point below is accurate. AX certificate is fine and is not UG-eligible, companion earns no miles. DL.com's handling of the certificate is deceiving