The SQL Agent account that is launching the CMD file probably has no QlikView license assigned. QV Desktop won't load/run the script because it will only run as a PE version.
Do you have a QlikView server? Then schedule the reload in QVS/QDS as a task to be triggered by an "external event". Use the EDX command line tool QMSEDX Enhanced to let the SQL Agent trigger this task remotely on the QlikView server. No QlikView license necessary.