Never had that problem before. Perhaps something happened in transit to Nagoya that rendered it undeliverable, like the label coming off or something...
After all, Japan has crazy label technology where you can pull off a label without ripping the box - maybe it wasn't stuck so good!
Since you got the refund already, it couldn't hurt to enquire about it never leaving Japan; you wouldn't want the same thing to happen again somehow. They have responded to me in English before and pretty quickly too.