Due to a bug in the Quartus® II software version 14.0 and earlier xcvr_diffmifgen.exe tool, the reduced MIF file is missing some RX PMA settings for Arria® V, Cyclone® V, and Stratix® V devices.
Device Family: Arria® V, Arria® V GT, Arria® V GX, Arria® V GZ, Arria® V ST, Arria® V SX, Cyclone® V, Cyclone® V GT, Cyclone® V GX, Cyclone® V ST, Cyclone® V SX, Stratix® V, Stratix® V GS, Stratix® V GT, Stratix® V GX
Area: Component, HSIO
To work around this problem you can use the full transceiver MIF file.
This problem is fixed in the Quartus II software version 14.1.