If you had a previous version installed e.g. any version prior version 10 then this could be causing the issue. If that is the case then remove registry entries related to QVS (you'll find it under HKEY_LOCAL_MACHINE -> Software -> QlikTech). That should solve the issue
With what user are you running the QlikView services? It should be a domain or local user with administrative rights on the server and not Local System. Sign in also to the Management Console also with a user with administrative rights on the server.
I had this same issue on a server install for a client. I did a standard install but the license would not apply. I checked the services and they were running as 'Local System'. I am not sure why as I specified the user during the install as I nornmally do.
Anyhow, changing it to the the local admin account fixed the problem and now the license is all fine.