You may notice that the Hiragana input source (used in Japanese) is grayed out and cannot be selected when using Kotoeri. This happens in both the Input Sources menu icon, and, in the Input Sources pane of the Keyboard preferences.
If you upgraded to Mavericks, and noticed that not all of your books were migrated from iTunes into iBooks v1.0, update to iBooks 1.0.1 to import the rest of your books.