MAX10 with NIOS does not start program code

Ok, I have just come back to this.

I decided to do a complete fresh build, new project folders, workspaces the whole sherbang. And it just worked as per the app note. Not sure what I may have set incorrectly along the way but it now works. My initial suspicion is that I had done so many incremental changes to Qsys, the quartus project and the BSP that maybe the tools were getting a bit confused, but maybe that is just finding an excuse for my lazy mistakes.