Well, without any insider knowledge and only going by Ryan Dancey's analysis:
The analysis seems to be well thought out, but may be off on one important point. It may be that the decision makers' environment is not so "information rich" in the case of PHB2. PHB2 is a new kind of product for the D&D line.
It's not a regular supplement like, say, Dungeon Delve or Open Grave, for which a good estimation of prospected sales can be made.
It's not a core book, so placing it at the same level of sales as PHB1 would also be wrong.
I assume WotC has tried placing it somewhere in between these models and convincing their (corporate) customers to do likewise. If they marketed it as "probably not as strong as PHB1, but much stronger than Open Grave", the environment is, by necessity, not as information rich as in other cases. Thus, the number of pre-orders may be less than accurate.
Add in the current economic climate - WotC will have no interest in overstocking - and the print run is not as accurate as it should be. Luckily for WotC, they printed to few, not too many copies.
Again, I have no insider knowledge, so my theory may be not worth the bytes it's made off.
Oh, and I apologise for binging this thread back to its origin.
