I applied at the beginning of March, with a trip scheduled for the last two weeks of May. I left Japan on June 1, and got my confirmation e-mail on June 5. Will not be back until next February, which is well beyond the 3 months I have to return. I am happy hear that they are getting faster now, but that does me absolutely no good. They really need to give more precise processing times if they provide such a short window for verification. It would be nice if I could just go to a consulate or embassy, but that would be too convenient.
Now I get to throw away my application and my obscenely expensive photos that were cut to the obscure size required for this waste of my time and sanity. Japanese efficiency does not exist when it comes to anything related to their airports.