Why does my application Nios code not run after remote update?

I get no error messages when I generate the programming files. In addition, when I generate a factory image that starts at 0x000000 in the configurator and download it to the board, the FPGA starts normally.

It is only when I try to use an application image that resides at 0x400000 in the configurator that things go wrong. The application FPGA code seems to load, but the Nios code does not appear to run correctly (if at all). The very same binary, downloaded and programmed into the configurator at 0x000000 runs just fine.

I am using the legacy epcs controller as the reset vector for the Nios and have implemented the boot code module using the Eclipse tool set.

I have come to the preliminary conclusion that the FPGA configuration code is loaded from the correct location, but the Nios code is coming from the wrong place in the configuratior.

I have resorted to updating the factory image but this is not optimal since there is no fallback if it is corrupted during the update.

I have had to move on to more pressing things, but I still would like to get this working.