It's some kind of weird married segment issue. The inventory is fine to HND. If I try multi-city search, I can get a more reasonable price but it wants me to stop in SFO on the way to Tokyo.

This may fix itself or it may not. I'm sure that part of this is that you're getting into holiday travel dates and they may be projecting that they can sell more of the higher fares than usual -- but YBM-only still feels like a mistake.