I have scoured to the ends of the Internet without an answer, so I come to the masses...
I just developed a new theme for a site I inherited. This install has 6-7 subsites. I installed the theme on the network and activated it on the main site and one of the subsites (dev site). There are two custom post types I defined in the functions.php but they are only registering on the main site and not on the subsite.
I tried the Custom Post Type UI plugin to see if they were even registering but they only appear on the main site. No menu items and as far as I can tell the subsite doesn't see them at all.
I setup a multisite environment on a separate server and the CPT are available on all subsites with the theme activated so I'm assuming something is goofed up with the other install I inherited, but I'm not sure where to start looking.
register_post_type( 'slides', array( 'labels' => array( 'name' => __( 'Slides' ), 'singular_name' => __( 'Slide' ) ), 'public' => true, 'show_ui' => true, 'capability_type' => 'post', 'has_archive' => false, 'exclude_from_search' => true, 'supports' => array( 'title', 'editor', 'thumbnail', 'revisions' ) ) );