Maureen, The info that I have on the CD is transcribed from the original permission to marry. Of course there is a possibility that info on him is missing or maybe he applied to marry under yet another name.

The second registration number is for the same marriage at the same place and same people. Sometimes this was because of a different name being used but in this case I do not know why it was done. It is not uncommon to have 2 or even three registration numbers for bdm where different spellings are involved.
It makes if difficult when there are different names used but surely he didn't have another one other than Owen or Eugene.
I will have another double check for you as soon as possible and see if I can find anything.
I was wondering if you know about the SAGS (society of australian genealogists) in sydney who have convict records...there may be something helpful on their site but you probably know about them already.
I will let you know if I find anything.............LIZ