Are you using NTFS or DMS for authorizing users to documents? You may have your documents to be distributed or authorized to "All Authenticated", so they indeed will reach to the AccessPoint, see ALL documents, then open only those where they have a license assigned.
Do the documents use section access? If you did, did you click on the Desktop, Settings menu, Document Properties, Server tab, "Filter AccessPoint List based on Section Access"?
Hope that helps.