It could be true you know, if Microsoft expected less sales than they've been getting their shipments might just have been too low.
It's not like MS know exactly how much they will be selling in advance, nor do they decide on shipments at the very last moment. Couple this with the known fact that Xbox 360 sales in Japan are not too high and a tendency for stores and manufacturers alike to strive for an inventory that is as low as possible even slow selling product can run out if demand surges.
And yes, selling nearly twice what you usually do does count as a surge in demand - even if the figures are not at Wii levels.
(As example: suppose Microsoft counted on selling 2,000-3,000 Xbox 360's a week for the comming months. Now sales are more like 4,000-5,000 Xbox 360's a week, so if they planned for a month or so of stock availability they'd have run out in 2 weeks instead and you'd get a shortage - even though they've not sold a gazillion of them)