Perhaps you know this already, but there are UTF-8, UTF-16, UTF-32,... standards. You have to make sure that you are using UTF-8.
Also, you need to set up the collates.txt file. If you haven't, perhaps that is what's messing up your searches. In that file, the lines are in alphabetic order. Each line specifies how to translate a group of characters to a single character used in the dictionary searches. You can look at the English version for an example of how to do it. You will need to add any missing Japanese characters in new lines in the correct alphabetic location. Again, this file must be in UTF-8 format.
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