Apologies if this has been asked elsewhere. Currently planning an AONE5 ex JNB using the Oneworld online planner and I've noticed that several flights aren't appearing when I use the planner that I can see when booking via the airline's website directly.

Namely, I've noticed:

1. JL006 from Tokyo to JFK does not show up (although AA flights do)
2. AA flights from JFK to Montreal do not appear to show as an option in the planner at all, but do on AA.com

I've tried different dates well within the 330 day time period with no luck.

Any thoughts? Can I still book these flights if I call AA and make a reservation over the phone?

Many thanks,
PC