So what does this mean for travellers? If we are headed beyond the intial US port, do we need to buy a separate ticket with a US airline and have to through a separate donestic check in? Will Qantas offer special connection support for say luggage transfer and delayed flights with AA?

Yes, this is normal for Jetstar and the reason why they are not a good option for business nor time-sensitive personal travel. I've learnt the hard way that they 1. fail and 2. don't fail gracefully. QF and VA may still have problems but they rarely fall apart so badly and, if you have status wit...

I'm VA Gold and 6 flights in the last month have taken a minimum of 7 days to be posted. VA processing has really slowed down lately. Hope the phone call  makes a difference.