In my book, the reason is that quite a bunch of people bought the game outside of Japan. This means:
a) more than the planned amount of people are updating
b) people are updating from outside of Japan
The result is that the updates won't run very well because there are loads of people trying to connect, and that a significant amount of those people is much farther away than it was planned. Taking that into account, noone needs to wonder there are so many Prologue owners experiencing updating problems.