I don't have the Japanese BD (which from all I know is just the Fortune Star upscale) so I am not sure. I'm basically working only on Hard Boiled at the moment since I am new to having to do everything involved with a hybrid (normally I had help) so it's a slow process.
Right now Hard Boiled's audio is synced. Now I need to learn how to do subtitles. I have CS5 and will need to create the Blu-Ray with Encore, so that's what I looking at now.