A very related thing happens (and is still happening--just happened a week or so ago) to me on my multi-city itineraries where I've actually got segments booked in Q and another that I've either legally waitlisted that clear in the 72 hour period or that I've upgraded using some form of upgrade certificate. If there is any segment in the record requiring a certificate to be collected, it will print it on all segment boarding passes. Luckily, it hasn't happened to me on transcon in a city without AS staff to see clearly what my fare basis was and know the rules. Of course, even in AS cities with AS agents...

... I was purchasing a ticket at ANC airport ticket counter (only because I was using aircare $off certificates) it took conferring with three different agents before they would upgrade the Q fare I was purchasing. First two agents (the one at the terminal next to mine overheard what I was trying to explain to the first agent and joined in to *assist* and *insist* that I was mistaken) involved kept insisting that I could only waitlist for first (unless using miles or a certifcate) as this flight was 2 months hence so sheer complimentary upgrades on Gold status did not apply. They had to go in back and took quite some time before returning. I gathered they were new hires, but you'd think that after even a few days on the job they'd have encountered an upgrading, ticket-purchasing (with all the city ticket offices closed) MVP Gold at some point.