Simple. Her label blew it with the way the album was released. The album just appeared in stores a whole 2 months after it's original release date. Not even a press release
But talking about Japan sales, I don't think anyone listed that you compared her to has sold as much as she did in the past (except Gaga).
Dangerously In Love - ~350,000
B'Day - 400,000
I Am... Sasha Fierce - 220,000
4 - 80,000
Bey DC3 did great numbers as well:
TWOTW - 200,000
Survivor - 400,000
Destiny Fulfilled - 750,000
#1s - 775,000
And I don't think anyone (again except Gaga) sold out the Tokyo Dome