Amazingly I have just found a very similar situation in some NSW records for my family. I haven't yet bought a certificate but I think the child was born before the marriage (there is a marriage) and either before or after the marriage the father's name was added to the certificate - One certificate number but 2 different names. The same person also has a second certificate number in his father's name - consecutive numbers.
Probably doesn't help your research - but it may mean a marriage took place somewhere/sometime. Could they have married outside Queensland?