Do old and new users belong to the same domain? Are their assigments made the same way (DOMAIN\USERNAME) Are you using custom directory or NTFS? Are the users Authorized in the User Document part of the QMC?
To check what directories are set up in the QMC go to System, Setup, Directory Service Connectors, expand and check which one has a username and password.
In regards to licenses, since QlikView relies on the OS for security (except when it uses DMS), you can assign licenses to users that are not granted permissions to read/list/write the file in the filesystem. You can check this:
If NTFS is configured: right click on the file or folder where the files are stored and check the Security tab to make sure that those users are allowed to see the file (or that they belong to a group that is).
If DMS, go to the QMC, Documents, User Documents, click on the document and the Authorization tab, and make sure users are there.