If the LM_LICENSE_FILE or XILINXD_LICENSE_FILE variable is set as a System Variable, VLM will read it, but if the value is changed to "set", the variable will be written as a User variable.
Depending on how the variable is checked, it may appear that the set operation has had no effect.
It is possible to manually change (set/remove) LM_LICENSE_FILE or XILINXD_LICENSE_FILE as a system environment variable.
On Windows 7 select Start -> Control Panel -> System and Security -> System -> Advanced System Settings -> Environment Variables.
From here you can edit the variables as desired.
In the Vivado 2014.3 release it is planned to have both the System and User variable values shown.
The System variables will be clearly shown as read-only.