Are you installing license manager using Creo 9.0 installation media or updating the exiting installation of Flexnet?
You may try replacing the Server and daemon lines in new license by copying the same from old license file and rename that as license.dat. Rename the existing license.dat to something else and place the new one in licensing folder. Try restarting the service for license manager service.
I hope this will help.
According to this Support Article
You have to have "FLEXnet 220.127.116.11 or later" installed for the Creo 8.0 and 9.0 license files. If you're running an older version of the FlexNET software, you've got to update to the latest or the license files won't work. I went through this just recently.