This is a source of frustration after moving to v2*.
On the previous versions, I had bookmarks for most of my repositories organized in to folders. However, some weren't placed in to folders, and were simply listed at the bottom of the folder list.
Along comes version 2, and the bookmark view is gone, replaced by a list of folders.
All repositories not placed in folders can now only be seen in a search or a view of 'all repositories'.