This turned out to not be a visual glitch for me. As I noted above, I’d called twice and was assured twice that everything looked great on Alaska’s side. I was still skeptical.

i checked in immediately at T-24, and found that I was nowhere on the waitlist, with ten other people listed. I immediately called Alaska, and the agent confirmed that she did not see me either, and did not see me on any subsequent flights on the same PNR.

While she escalated to a supervisor, I checked ExpertFlyer and confirmed that the two available J seats were still available. Ten minutes later, while still on hold, I confirmed that I was now top on the waitlist, but the previous top two had now disappeared and ExpertFlyer now showed J0. On top of that, my seat was now two rows back.

Agent came back on the line and told me that the sup was able to get me on the waitlist on the first segment, but any subsequent segments I would need to check with the gate. Kind of a damned if you do and dammed if you don’t situation - I could have her attempt to fix the other four segments and potentially lose what seat assignments I had, or check in at the gate, which meant that I would certainly be out of any window at that point, having even possibly MVPs already having been upgraded.

i opted for her to give it a shot, and the sup’s way of solving it was to split all of the segments other than the outbound to a separate PNR.

This was all during an hour & 20 minute conversation with Alaska. They did acknowledge having seen this occasionally since they implemented outbound/return same flight numbers. In my case it was AS1078 SEA-IAD-SEA.

They assured me they submitted a ticket with IT, but could not provide me with any ticket number.