NIOS II won't run from power-on

If you have a scope available, using FPGA config done as a trigger and look at the data output of the Flash. The EPCS controller should be loading the data from the flash and there should be a long string of ones and zeros ( your elf code ). I've never had this issue, so I haven't looked at how the elf is loaded, but it will most likely be in small bursts because the CPU is executing code at this point.