How do you install the 1.2 license? I think it needs a separate license server.
Unless there’s something wrong, you should be able to install it like usual:
http://www.thinkboxsoftware.com/license-server-configuration/#Updating_the_FLEXnet_License_Server_to_Use_a_New_License_File
It shouldn’t require a separate license server. What problem are you seeing?
It was saying that it didn’t support v1.2 so I uninstalled the lic server. Re-installed using the Deadline 6 lic server binaries and it worked.