Problem: I organised most of my layouts into folders using the Preferences screen. Everything worked perfectly, and I found the folders that I had created, with their layout files, as subfolders in the Layouts\Folders directory, with the position of everything neatly listed in order.xml.
When I Backup the configuration, however, the Layouts\Folders directory is missing from the zipped backup file. I restored the Backup onto another notebook, and noticed that while the Layouts\Folders directory was missing, the order.xml file still listed the folders and the layout files in them.
The Layouts\System directory, by the way, is there in the backup and in the restored configuration as it should be.