An an ex-bankie I am able to answer your question. If the system was offline or there was an issue with its processing for whatever reason, the bank dumps/captures all those transactions into a secondary system, which is like a manual back up. They hang around there until the problem is fixed and then it is processed and checked through a back up system. There is some kind of manual process involved. I imagine their systems could be under pressure if the banks have re-routed transactions away from servers in the CBD, so it could be this or just simple phone line issues that caused it, but never fear, they *WILL* take your money!!!

ETA - it's helpful to think about an EFTPOS transaction as an exchange of a chunk of info between your bank and the merchant's bank.