In both the root and the mounted folder all subfolders are also searched for .qvw files. In this case the same file is found in both locations. To stop this I would suggest moving your mounted folder to a different location - even a different drive if possible.
When I set up a server I tend to create a folder structure like this:
I then set the Root folder in QVServer to be the root folder and then set up separate mount points for each business unit and the system folder (where ops monitor etc. resides). This way any folder can be unmounted from QVServer in order to remove it from Access Point - without having to physically move any files and folders.
If you decide to move your Root folder you should move any .pgo files from the existing root folder to the new one when you do so.
Hope that all makes sense.