Thanks all for all the helpful comments.
Yes I agree Intr must stand for Interior - I didn't think to look back at other pages as the abbreviation was used elsewhere on the same page, but after going back several pages I did find an entry "Interior to Parramatta" and there were also several "Intr to Parramatta" references.
It makes sense because in those days anything outside the Sydney township was considered "the Interior".
Dawn, thanks for your suggestion of contacting State Records. I will do that to see if I can get more information. The Entrance book doesn't give any indication of why John was incarcerated. I did check the archives guides, and the description there of these books indicated that there should be such information and a lot more, but this particular book doesn't have that sort of detail. Perhaps different gaols kept books of different detail. Oh and yes I do know the location of Brisbane Waters, but thanks because it could be a wild goose chase for anyone who didn't realise!
John arrived in 1835 on "England" - he was at Liverpool in 1837, followed by Bathurst in 1839, where he first got his TOL. He next went to Botany and then Brisbane Waters in 1840. His TOL from 1839 was updated with each move showing his new location. In February 1841 he applied for permission to marry a Mary Green and there are a couple of records of this application and banns of marriage were pronounced. However it appears that the marriage did not go ahead for some reason as there is no record of the marriage and shortly afterward in August 1841 Mary married a Samuel Pearse.
John eventually married Catherine Moran in 1855, by which time they already had 6 children (!) though 3 had died. The first, my g-g-grandmother was born around 1845 in East Gosford.
I have only just become aware of this episode in 1843 in between the time he broke up with Mary and took up with Catherine, thanks to the records becoming available on Ancestry.
I will post back if I hear anything further from State Records (might take a few weeks!)
Thanks again
Anne