Unable to burn my project through the "NIOS Flash programmer"

I'd try building something where main() is just 'return 0;' - that is about as small as things can be!

One problem is that you don't really know what the IDE (etc) is actually doing.

My build system directly runs gcc and ld with a linker script that contains exactly what I want.

It might be that the '.exceptions' section contains a the interrupt code - which should be at the address specified in the sopc builder (cpu property).

However the linker could generate a jump instruction at that location - in which case the interrupt code could be anywhere in memory.