I've had the same issue as the OP a couple of times. Both times my issue was due to being upgraded on a UA segment. There currently is no workaround due to the way UA issues the upgraded ticket. I don't remember the details, but the gist (as I understood it) is that a separate UA department handles the reissue and this impacts the entire itinerary. Unfortunately I was not able to write down the details, but I was told by a CO rep that the best thing to do is not be transferred but have them call their support number. Someone may be able to expand on the details, but each agent has the number of a supervisor in the other airline they can call for issues such as this. In this particular case they can't issue the ticket anywhere but the airport, but they can confirm upgrades and seat assignments.