Code in tightly coupled memory

Have you checked what the elf program headers say? (objdump -p)

I've had the JTAG loader correctly loading code to multiple memory areas.

But I did have to hack at the linker script to get the code linked into the correct places.

The Altera linker script (9.0) appended all the sections onto the end of the normal data, and added function calls to copy the data into the relevant areas into the startup code.

Most of my code is linked using a completely custom linker script and loaded into internal memory blocks via a PIO interface from another processor on the board (no JTAG in sight). Once the code is loaded we remove the soft reset from the cpu.

In fact I have 2 nios - and one releases the reset on the other.

All works fine!