This doesn't sound like a Qlik Web Connector issue, rather a standard QlikView Server / AccessPoint one?
For a document to appear in AccessPoint the user must have Active Directory permissions to the .qvw file (usually by virtue of folder permissions).
The CAL permissions dictate whether a user can open an application from AccessPoint, but it is AD that dictates whether it appears.
The correct setting up of folders under Server settings is also a factor, and the Browsable tick box next to it.
Is it that some users can see the document and others can't, or can no one see it?