Well, this tells me that it's not a GW issue, so it must have to do with my own add on sceneries. That's important information.
It seems like an exclude issue to me too, but I haven't found any excludes with suggestive file names, and I can't think of any reason why a scenery designer would exclude the city unless they were replacing it with something better.
There is a SanFran bgl file in NAMW that's different in GW than the stock FS9 version, but replacing it with the stock version doesn't restore the city.
I found two SF sceneries on line and tried installing them, but they don't show up. That's especially confusing because if there was an exclude file, they should show up as long as they're higher in the scenery stack, but they don't, even when they're right...