Yeah, this is a common problem. Few people are aware of this benefit.
I had one recently, a 5-segment reward trip, where 3 out of 5 upgraded via EUA ahead of time. Checkin didn't add me to the list on the remaining 2. EUA cleared one of the remaining two before getting to the airport, leaving only one to reconcile.
SFO agent was unfamiliar with it, but called in. Helpdesk was also unfamiliar with it, and then she started asking me how I got all these upgrades on an award ticket. I told her to hang up on the Helpdesk, since I didn't want my four (4) upgrades to be revoked by some rogue Helpdesk agent, creating some bigger problem.
She then figured it out and typed for a few minutes and got me on the list.
The previous time, I received no EUAs, and no additions to the list. Nobody on the phone could help, and the airport couldn't help, despite a 3-agent SHARES huddle (3 agents, 1 phone, 1 green screen).
This is one of UA's most poorly executed benefits. And given how poorly UA executes most things, that's pretty bad...