You need to add to the QlikView administrators, only the users that should have access to the QMC (QlikView Management Console - in ther server). So you need to be careful because they can control the server.
How to use use the QV Desktop to open the dashboard? Do you use it to connect to the server and open it or you browse to the windows folder and open the .qvw directly?
The accesspoint will check windows permisssion in the .qvw to let you see it there. You need to check the file permissions.
Also, the QlikView server will only map the root folder and mounted folders. Only the files that are there will be visible in the accesspoint.
You need to go to http://yourservername:4780/qmc -> Then system tab, QlikView server - > Folders and check which folders are mapped there.
Hope it helps,