Due to a problem in the Quartus® II software version 15.0.2 and earlier, the setting of Configuration device I/O voltage under Device and Pin Options may revert back to Auto. You may see this problem when you change any settings of Device and Pin Options except for Configuration device I/O voltage.
To work around this problem, set the Configuration device I/O voltage after changing other settings.
This problem has been fixed beginning with the Quartus Prime software version 15.1