If you're flying SM partners you may have to work carefully with the SM agents on the routings. Sometimes it will price each part very high esp if using your stop-over and OJ. But if you are following the routing rules correctly, have the agent call someone at the pricing desk to work on it.

I've had this problem quite a few times intra-Asia, so make sure someone works on it to get it at the right level of miles. Good luck.