You may experience the above error when the Memory Format option is set to Registered DIMM for your DDR2 UniPHY-based controller in the Quartus® II software version 12.1 and later. The error occurs when the Number of chip-select per device/DIMM option is set to 1.
Device Family: Arria® V GZ, Stratix® IV E, Stratix® IV GT, Stratix® IV GX, Stratix® V E, Stratix® V GS, Stratix® V GT, Stratix® V GX
Area: EMIF, Intellectual Property
The workaround is to generate the DDR2 UniPHY-based controller with two chip-selects and ignore the second chip-select signal from the controller.
This issue will be fixed in a future version of the Quartus II software.