I have an answer for you...but its complicated, hence why Qantas Group hasn't solved it yet.
First up, JetStar changed the way they interfaced with the QF FF Database mid way through the year.
Prior to this change, you could make an online booking the same way you do at Qantas.com – that is; do flight/date requests and add you FF number to the booking once you have selected the segments you want. This would automatically associate the booking with your QF FF number, populate the form information, and afterwards, you could log in to either JetStar.com.au* (as a QF FF) or Qantas.com and see your advanced JQ bookings.
Now, since the change, the system will still ask you for a QF FF number after you have selected your flights (when you enter your personal details), but it will not cross reference the number with the QF FF database (and therefore not populate the form). So while you will receive a .pdf itinerary emailed with your frequent flyer # displayed, you can not log in to either JetStar.com* or Qantas.com as a QF FF and see your advance booking.
So…next step is to try and correctly associate the PNR with your QF FF details. Neither the JetStar nor Qantas website are able to do this via their booking management screens; you will receive an error message. Calling JetStar is no use either, as they can see your QF FF number in the booking, indeed once you have flown, your QF FF Activity will show the JetStar flights - but no one at JetStar is able to fix the system by properly associating the booking with QF FF. (Most of them can’t understand what you are talking about.)
Qantas Frequent Flyer is also unable to help, and suggest that you contact the airline you made the booking with. (Hmmmm!)
Anyway, to solve this endless loop next time, you have to first log in to JetStar.com as a QF FF before you do anything else! That’s right before you even start looking for flights/times, log in.
Admittedly, I constantly forget to do those extra key strokes/page hits before I start booking flights, and have many future flights that I worry I will forget about, because they are not in my Qantas.com FF future bookings screen.
* NB: the issue came about, around the same time as the Australian website’s integration with the Asian one.