A problem of using sdram

Just like mountain was saying you may have to put a phase shift on the SDRAM clock (it's best to think of it as a time shift though). If you look at any of the standard or full featured hardware reference designs installed with Nios II you'll see the shift I'm talking about (note that shift isn't necessarily the same amount that you need if you are using a custom board).

Also if you have Nios II 5.0, try opening the SSRAM memory component and click on the link to the readme.txt file for it (or find it in the documentation folder). It gives a really good explination about the phase shift needed for SSRAM and the theory can be carried over to SDRAM.