Hi Chris,
Just noticed that under the reset options for the format, the top reset line is missing the four times that can be seen on the second line. This indicates that the custom capabilities have not been installed correctly. And hence why you do not see the settings under 'Course format'. This will also mean that all teachers etc. will also not be able to edit the settings. When installing did you go to 'Notifications' under 'Site Administration'?
Gareth