Does the nios2-download tells you that the processor can not be paused? --> check the reset signals for DDR2 controller (High Performance DDR2 Controller with Altmemphy has a reset_n signal as a top level port for the SOPC Builder System).
Does the nios2-download tells you Verify Failed? --> If you are downloading to DDR2 there may be problems with signal integrity. Try to build a memtest to run from internal memory.
I assume that by "download" you mean that you are trying to download a program. I would not give to much confidence to simulation when a designed based on Altemphy or uniphy are included in the project because these two *phy do not support post fitting simulation (found in the user guides).