Permalink Structure Custom Post Types

For some reason my new permalink structure /%category%/%postname%/ will not work with my custom post types. I have changed the .htacess file to reflect my structure on my server. I have also used the rewrite parameter when defining my custom post type. The weird thing is that I don’t get a 404 error or a wordpress page cannot be found error. All that is returned is the header and footer of the site. The content is just blank.