Nios II System download problem!

It looks to me as though the 'linker script' being used isn't assigning all the program sections in the object files to appropriate addresses.

In addition the build system is including large tracts of code from libc that you just don't need for simple embedded code blocks. However the address overlaps you are seeing look like they are due to several object sections being given the same base address, not running off the end of the available memory area.