I have run the script through SSH using Putty to type in these commands. I first typed the set up command and rebooted. I then tried to configure with the argonone-config command, setting to both the 1 and 2 options. Neither work from what I can tell as the fan has only come on in the initial boot up for a second or two. I do not know if my Pi just hasn't got hot enough yet for the fan to kick in but I fear this could be a more serious problem.
