In my experience, the "manage my booking" feature differs between the JAL US site and the JAL JP site.
For my upcoming flight, I can only see my partial reservation with just my US legs on the JAL US site, however, when I switched to JAL JP, I can see the full trip
So for those who are having trouble seeing your JL operated flights, change the website region to Japan, English and look for the "My International Booking" link