Doesn't matter. What matters is that you must check in with CO to be added to the waitlist for battlefield upgrades. Checking in with UA (or any other airline) on an interline ticket doesn't trigger the event needed on the CO side of things to get added.

And resolving that is something that the airport agents handle, not the phone folks.

All the phone folks see is if you are in the EUA "queue" and you almost certainly were.