Due to a problem with the Altera® daemon (alterad.exe) version 14.0, the Quartus® II software version 14.0 does not recognise the license file. This happens only when the license server is on Windows and the Client (Quartus II software) is on Linux.
To work around this problem, point the alterad.exe in the license file to 13.1 version instead of 14.0 as shown below:
VENDOR alterad " <quartus_13.1_install_dir>\quartus\bin\alterad.exe"
This problem is scheduled to be fixed in a future release of the Quartus II software.