Nios 1 to Nios 2

Did you try to program the flash manually, not through the GERMS but with a simple stand alone program that you write yourself? Maybe this can be a help to understand the problem. At the end you can convert that little program to a home-made boot loader.

I use also legacy mode, but not with the altera provided lib. I only use the excalibur.h file to now where the peripherals are. I now it is some more work in the beginning, but it can be faster to detect problems like this.