That usually happens when a folder within the root folder is added as a Mounted Folder. Go to the QlikView Enterprise Management Console, System, Setup, QlikView Servers, expand and click on yours, and on the right pane select the Folders tab. Check that there is only one Root folder and that the mounted folders, if any, are not under the same folder structure that the root has.
The reason is that the root folder will show all QVW files in it and within its subfolders.
Hope that helps.