Does it have furigana, I find that interferes with the dictionary a lot. Pops up fine for me, just doesn't let me select the word I wanted. Is it set to Japanese language as per the metadata, ... is it EPUB or KEPUB? For Japanese mode only KEPUB works for me.
Can't imagine how "In Book" works, does it still let you select word boundaries? (Actually my H2O just crashed on me when trying to go in book, but it may be related to the
enhanced japanese dictionary I'm using)