Permalinks not working using wordPress Networking with custom post types

Hay All, I’ve setup a WordPress network and have a couple of websites. Within these ‘sub-websites’ have a created a new custom post type called ‘courses’. When i create a new ‘course’ a sample permalink would be

www.mysite.com/site1/course/my-course-name

However, this doesn’t link to the article in the question. Is this a normal error with wordpress?

How, can i fix this? I think there’s an issue with the .htaccess file WP generated for me.

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