I can think of several reasons (but they're all just guesses):
- The initial Kindle version is so poorly formatted it drags down the book's rating overall.
- The publisher is coming out with a new edition or version of the book or of the Kindle version of the book.
- The publisher has a scheme that calls for no Kindle version of the book be available, at least for some period of time (e.g. so as not to cut into sales of a pbook edition).