OK, a little follow up. Just got off the phone with AS and as noted above "the system" sees that I'm on the waitlist, but there is a glitch showing it on the flight details. Rep was working with supervisor to investigate and is going to call me back.

Initial thought was that since the fights have the same flight number both directions and these are same day turns which is causing the error. For example, SAN-JFK is AS180 and JFK-SAN is also AS180. So, I'm waitlisted for the outbound AS180, but not the return AS180. The reservation with both legs showing I'm waitlisted has different flight numbers for each direction. And, the reservation mentioned in the OP showing neither leg has now added the waitlist to the outbound leg.