We have a system of folders and subfolders set up in our Junxure Documents.  When a document is saved in a subfolder, it does not show up when the root folder is selected (you must double click the root folder to expand the view to show subfolders and then you must select the appropriate subfolder).  This makes it look like nothing is in any of the subfolders unless you expand the root folder and click through all subfolders to manually to find a document.