Bumping an old thread, as I've been running into issues with this myself recently. I'm an MVP Gold, and had an in-cabin pet on a recent R/T reservation.

Up to and including the day of departure, when viewing my PNR on the Alaska website it shows me waitlisted for first class.

However, after check-in, I am NOT on the upgrade list. This has been confirmed by agents at the airport. The check-in agent was able to add me back to the waitlist, though F was full so it was a moot point.

I've got an email inquiry in to Customer Service for details, but it would be interesting to understand what's happening. For both of my flights, I feel that I likely would have been upgraded had things worked properly.

There's also no documentation on the Pet page indicating upgrades are not possible. (And, my memory is hazy, but I feel like I have been auto-upgraded in the past with a pet on my PNR. Maybe it's just day-of-departure that doesn't work?)