I've found myself in a similar situation, where a SYD-CBR hop was added to the itinerary and received an eticket email. Yet CMT did not have a ticket number for that last flight, all the others did. On closer inspection the eticket number had not changed since the previous change.
On calling Qantas, went through the process of putting the booking on the 'ticketing queue' and wait 48 hours, did this several times while keeping watch on the other flights (on AT/RJ and JL) with no new eticket issued. Received various reassurances that all is good and reasons as to what was happening and why - including a re price requiring 167000 points payment, didn't proceed with that option. After about 10 days no new eticket, but all the other flights are intact and ticketed (status on JL website is 'ticketed', the AT and RJ website still have the ticket number listed), an agent mentioned that unticketed status of the SYD-CBR flight will not affect the non QF flights and that the new eticket will be issued 'soon'. Who knows how accurate that is.
Anyway that was Monday and it is around 2 weeks since the last flight was booked. I'm giving it a little while before calling again, while being eagle eyed for changes on the other flights. None have changed to date..