Flash programming issue with stratix kit development

Did you take into account the information provided on page 2-19 of the reference manual. Apparently there is a rotary switch that needs to be set accordingly. Also, you need to make sure you program the FPGA configuration and your software image into the appropriate location within the flash. It looks to me like you're trying to program the FPGA image, software image, and read-only zip filesystem all into the same location in the flash. Not going to work.