I'm in the same situation - 1360 SCs and 40 JQ SCs owing (NTL-BNE-NTL). Flights were six weeks ago, points claim went in just under six weeks ago.
Had a lengthy phone conversation with both Qantas and Jetstar today. The main issue for me is I used mobile boarding passes which are no longer valid (didn't save them to my wallet unfortunately). They told me if I can get them off Jetstar they'll credit them manually.
Called Jetstar - no can do. They've raised a case and will get someone to write Qantas a letter saying I boarded both flights - but that will take 10 working days.
What I'm most annoyed about is I've had a points claim in with Qantas for nearly six weeks (it was manual request via email too because the online tool wasn't working) - what exactly have they been doing for the last six weeks? Both airlines implied that they'll start working the problem today - they should have been doing this weeks ago.
It sounds like it's Jetstar's fault - and to be fair I recently flew JQ NTL-MEL on a QF codeshare (international ticket) and those points credited within 48 hours.
It's not about "admitting" JQ is part of the QF group.
JQ use a totally different res system and thus things like sending info across to QF's systems to be processed etc require other processes to extract from one system, then import to the next, which are probably done as batch runs at certain times for various reasons. It's not quite as simple as perhaps it should be,
AA use a different system too, and they manage to credit within 24 hours. Not to mention Avis, Woolworths, credit cards etc. This is an airline owned by the same parent company that specifically advertises Qantas points / SCs as part of their bundles. The fact the QF coded flight credited quickly suggests it's a ticketing issue, not a boarding notification issue.
I've got almost six months left of my membership year, so it's not like I'm running out of time, but I've got a few domestic trips in the next few weeks (one on Friday) and I'd like to use the business lounge. Sadly it's probably going to be these QF flights that get me over the line. Useless Jetstar.