When configuring node types for a workbench, the order in which you configure them matters. But it should not matter. For example, if your content app supports folders and some custom node type, you need to configure the custom node type first. Otherwise the Tree view displays only the folders and the List and Thumbnail views display the folders only (if there's any). This is a problem because in a typical content app you have at least two node types: folders and your custom nodes. Have to be really careful with the order.