JAL has a variation of married segments I refer to as divorced segments and it has become more common of late. A "divorced" segment is not allowed to be booked as part of certain types of connecting trips. Typically when I have seen it there is a connection in Japan where at least one leg is an international flight. This sounds like it may be what you are experiencing. If it is you will have a very difficult time trying to marry the divorced segment, much as you would if you were attempting to break a married segment. The system is not going to allow it. It would have to be someone manually overriding the restrictions to force it through, if this is even possible and allowed.

JAL married/divorced segment restrictions are dynamic and can change, so the restriction may be lifted at some point. Sometimes there is a pattern as to when they change.