If under the top menu the first item is a site and the second item is a folder right clicking on that folder and clicking Mark Folder as Read marks the site as read instead of the folder. If instead of right clicking your left click on the drop down arrow and say mark as read it marks the folder as read. It is like it does not understand what you clicked on and although it brought up the folder menu it performs the action on the previous site.
Now if you have a site, followed by 2 folders in the navigation menu right clicking on the second folder works fine, but right clicking on the first folder has the problem.