I was travelling to Melbourne (MEL) fron Dhaka (DAC) by Malysian Airlines couple of weeks ago. Everything was ok on our side. At check-in counter they were unable to print my boarding pass. They told me its just not there and I can't go. Then I talked with their supervisor and asked for an explanation. At first he was unable to answer any of my questions. He then started making phone calls to their office. After half an hour later he asked me for my old passports. Which was already there anyway. Then they printed my boarding pass and let me go. Both sides immigration and customs were swift. Nobody asked anything special. Never had this kind of problem before. Now I'm wondering what was the actual problem.
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.