I have a similar issue others have had with the attachments pane not showing up in the add/edit post for a custom post type, but with the difference that I never had the legacy version installed. I had WordPress 3.3.1 and Attachments 220.127.116.11, and my attachment pane was showing up fine for posts, pages and my custom type "resources". Then I upgraded to WordPress 3.5.1 and Attachments 3.5, and now the attachments pane only shows up for post and page adding/editing. It won't show up in the editor, and the posts I had added that included attachments no longer showed their attachments on the site. I tried downgrading the plugin back to 18.104.22.168 but it made no difference.