@Kest: IIRC, when Amazon introduced the Kindle in Japan they added XMDF support to KindleGen. Maybe all the books that work on your Kindle were converted from the XMDF format.
Try finding a free XMDF book on the Internet, unpack the book folder and convert it with KindleGen or create one from scratch following the instructions in Appendix D of the
Kindle Publishing Guidelines.
It also couldn't hurt to also test the working Japanese books and your home-made books with the Kindle for iOS/Android/PCs apps to exclude eInk Kindle specific issues. (I'm assuming that you've installed the latest firmware and no homebrew apps that might interfere with the rendering of Japanese characters.)
Also remove all stylesheets and inline styles from your home-made books before you compile them with KindleGen to find out if this makes any difference. If it does, post the relevant stylesheets.