I did not change anything concerning Japanese input methods. This is handled by Java and OS itself. Did they work in the previous Java 8 update? CT sets the target language locale for Java based on the project target language so make sure that the target language is Japanese.
I found a website reporting the same problem. It seems to be due to Java 8's latest update 51.
Maybe I should go back to the previous update, with which I saw no problem.
If it is essential in your workflow, please downgrade to Java 8 (previous update of Java 8) until Oracle solves this issue. Do not downgrade to lower than Java 8 on Mac.
In the latest update, I can't type in double-byte spaces in Japanese (through Japanese IME). This is a serious problem.