I recently did a fresh install of 13.10 and enabled Japanese language support.
In the past this seemed to work seamlessly with my other keyboard settings when I set up my Dvorak keyboard.
But this time when I toggle the IME on it uses the standard QWERTY layout. Typing English uses the Dvorak layout as I expect.
This just worked for me in the past to the point where I stopped paying attention to what the underlying IME is and I don't recall any special steps other then choosing my keyboard layout and enabling Japanese.
Any help would be appreciated!