I am having the same problem. I have the DSK kit which has the Cyclone 2 EP2C70F672C6 chip. It also has the Micron MT8HTF3264AY-40E; 256 Mbyte, 32 Mbyte x 64, 167 MHz, 1.8 V, 240-pin, non-ECC, un-buffered DDR2 SDRAM DIMM.
I am trying to R/W this dram by using the example design generated when using the DDR2 IP core. I don't what to use NIOS. I have assigned the pins according to the manual. The error message I get is:
Error (172078): DQS I/O pin "ddr2_dqs[0]" does not feed a Clock Delay Control block
Interestingly, I went to the Production Tests that were installed when I got the board. Once such test does test the DDR2 which passes. Unfortunately, Altera only gives the .sof file. There is also a NIOS "standard" design. However, if one looks at it the design is only using 16 bits for the DRAM. Rather worthless since it has 64 bits!
So, I'm stuck as you are.