ELF download behaves differently than initialized hex

Are you sure the sof file has been generated with the updated hex files?

It seems you have some memory section not correctly initialized: then when the code hits there, it hangs.

Although I believe this is not your problem, you may try to add the following calls in the very beginning of your main() for every code/data segment which is possibly not mapped to the default linker sections.

ALT_LOAD_SECTION_BY_NAME(<name>)

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2) Does anybody have suggestions of how to debug this? Right now, all I know for sure is what I have written above. The software works, then it doesn't. I can't send debug messages out the JTAG UART because I'm not using it. Is it possible to use the Eclipse NIOS JTAG UART console without downloading the ELF? if so, I haven't figured out how.

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After you loaded the sof configuration, open a Nios shell prompt and write 'nios2-terminal'

If you want full debug functionality (step into code, start, stop ...) you can still use Run As... in Eclipse, but you must disable the default Reset and Download features, so you simply attach the debugger to the running program.