When you select the Micron MT41J64M16LA-15E memory preset in the DDR3 ALTMEMPHY based controller, the data width is incorrectly specified as 8 bits by default, but in fact, this device is a 16 bit wide device.
Device Family: Arria® II GX
Area: Intellectual Property
IP Product: DDR3 SDRAM Controller supporting ALTMEMPHY
You will need to manually change the data width from 8 bits to 16 bits.
This issue is fixed in the Quartus® II software version 12.0.