NIOSII addressing for 32 bit wide SDRAM

Can you copy your test code into this post just to make sure it's not a software issue. Also when you say that you dropped the clock speed down to 50MHz, you left the SDRAM operating at a faster clock speed correct? DDR-SDRAM has a minimum clock frequency of 77MHz if I remember correctly, DDR2-SDRAM minimum frequency is 125MHz I think.

Also I still highly recommend simulating this design, it'll show you what the accesses look like on the fabric and will not be affected by timing issues. The Nios II software will get pulled into the simulation so there isn't much you have to do besides run a macro or two in Modelsim before starting the simulation.