CR would definitely stand for capital respite, in so many shipments of convicts the majority were were those under a hanging sentence that was commuted to life.
I have a many times great grandfather who came out on the Third Fleet as a boy in chains. By the time he had entered his teens he had escaped Sydney and was heading south and eventually ended up in southwestern Victoria.
I have tried to find him in convict records but he used at least 2 names, Lawrence Murphy and Edward Pearson. (most likely both false)
In 1868 he was charged with stealing a sheep carcass from a butcher's shop in Collingwood but appears to not have been convicted. If anybody else knows anything about my dodgy ancestor I am very eager to hear about him. He was living in southern Vic. with the Aborigines at William Buckley's time but unlike Buckley avoided recapture and died as an escaped felon.