We're having problems getting any of the course options available within the SharePoint LMS, the features have been activated within the SharePoint LMS at every level we can find (IE landing page, within the course) , but whenever I go to create a course,

This might have happened if you missed the installation step with global features activation.

But on the whole there are three locations where you should check the settings:
1. Global features (central administration)
2. Organisation features (site actions-site settings - organization features)
3. Course settings (site actions - course settings - course options)