Hi Jonathan and Mark: I have been doing some tests, and I realised that the issue could be related to how we name our custom post types. I created 2 custom post types. The custom post types are created without the use of any plugin. One named 'cooking-class' and the other named 'recipe'. I registered attachments instances for each post type separately.
The attachments metabox appeared without any problem for the 'recipe' post type, but it only appeared after I publish a post for cooking-class'.
Seems like the '-' in how I named the post type is causing the difference.
Tested this using a clean install, all plugins deactivated except for attachments.