Any update on this guys. I can't get it to work with custom post types and it wouldn't work on your own demo with custom post types. Great plugin but this would be a much need feature to fix. I'm using this in Multisite and it works fine on the root blog, however it won't work for other blogs on the network (custom posts or posts, pages, etc.). One thing I also notice is when you go to use it on one of these blogs, it defaults to "Customize" versus "Default". When you try to add a widget when using customized and save, then update it disappears from the sidebar. Hope this helps.