Don't give up. I'm just about to start my disputes with Amex and this thread (plus a few other places online) have been a great knowledge bank.
You should lodge a complaint with Amex via
Customer Relations Manager, GPO Box 1582, Sydney NSW 2001. Others online have described a positive response via this method, when they initially had non-acceptance of chargeback requests through the normal transaction dispute pathway online.
If not successful, certainly follow up with the AFCA (ombudsmen). You have nothing to loose but potential to gain.
It has been mentioned that due to the structure of Amex, they would have to essentially absorb the loss themselves, unlike Visa / MC who can seek funds from VA's merchant bank, so then VA's bank has to accept the loss and essentially become the unsecured creditor.
Amex may not like it, but the card schemes are there to protect cardholders and give confidence to use the cards. It has been argued elsewhere online that insolvency proceedings of a merchant do not rescind these chargeback protections offered by the card schemes.
The chargeback reason "goods and services not received" is available to be used, and is applicable for companies that become insolvent too. You can use this document to find details of that chargeback code...
Amex Chargeback Codes. The interesting part is for airline merchants, Amex suggests one suitable bit of proof for a merchant to reverse a chargeback from a cardholder in this instance is proof the flight in question was available during airline bankruptcy proceedings...ha!
I could be mistaken but I am wary that the "relationship" Amex has with Virgin could also be a reason that chargebacks are not being found in favour of cardholders in this situation. Certainly the setup of Amex having to take the financial hit with chargebacks with no recourse to subsequently claim from VA's merchant bank would likely be the main reason.
There is also this document..
Affidavit in Federal Court. Submission by an accountant and liquidator from Deloitte (VA's Administrator). They mention if conditional credits are not used or not accepted (my understanding is you probably would have to write to VA to say you don't accept them as a remedy), chargebacks are a valid method for customers to claim money back. Might not be the easiest document to read but I think it is useful.
In the end, I think a referral to the AFCA will result in a successful chargeback in many instances...just requires a damn bit of effort unfortunately.