Upvote:3
While we can never be sure of the exact cause, the issue appears to be related to a failure of the Advance Passenger Processing (APP) system.
All airlines flying to Australia are required by the Australian Government to check all passengers' immigration status at check-in using the APP system. The check-in agent submits your passport details to the APP system. The system then checks, among other things, whether a valid visa has been linked to that passport, and returns a Board/Do Not Board response.
It would appear that initially the system returned a Do Not Board response when you were attempting to check in. This is why a boarding pass cannot be issued. Normally this is due to the passenger not having a valid visa, or forgetting to transfer the visa across to a new passport when it was renewed. However, based on your comments, it is possible that an IT issue resulted in a Do Not Board response.
Whenever there is an issue with the APP check, the airline can contact the Border Operations Centre help desk in Australia for help. This appears to be what happened: they were able to resolve the issue, scanned your passport again, received a OK to Board response from the system, and print your boarding pass accordingly.