Paging sfogate?
When I did it, the gate agent seemed to have to handle the request manually. That may have been because Y was full as well, and she knew that if my name was next on the list for an available Y seat that I didn't want it, only F. Somehow she got it to work.
And by the way, the correct terminology in this case is "standby" not "waitlist". The waitlist works in advance, up until 24 hours before departure. The standby list (whether the flight standby or upgrade standby) is for at the gate.