Thanks,
The flight numbers are different e.g. Melb to Cairns is JQ34 & Cairns to Tokyo is JQ25. However, it's all under the same booking reference as it's booked together. So fingers crossed.
Seems like there are a couple of JQ domestic flights from Sydney & Melbourne that fly into Cairns International terminal during the morning and then funnel passengers onto JQ flights to Tokyo and Osaka in the early afternoon.
It's good to see that this may have all been finally sorted out, as having to use the Cairns domestic terminal was a bit of a pain e.g. getting luggage and checking into another flight etc.