In regards to your first question, it seems you have the same folder as root folder and mounted folder. The root folder will respect all subfolders and will show them as subfolders in the QEMC, Documents section. Mounted folders appear with a red light indicator in the folder icon. Are you running the latest update of the QV10 Server? (SR3 build 9061).
The Accesspoint does store some cookies in your browser, PreferredClient (with value Ajax in my case) and View (with value Details in my case) among them. So you will need to check that your cookies from your server running the accesspoint are being accepted.
Hope that helps.