Ethernut is storing it's config data in the last page of the flash controler. For the At91Sam7x256 everything is ok, but the At91Sam7x512 has 2 flash controlers and the config is not stored - as supposed - at the end of the second flash controler but at the end of the first controler. This results in errors when a program is bigger than 256 KByte because saving the config overwrites program data. I haven't found any code to use the second controler at all, just increasing the pio base address isn't sufficient here.
By the way it would be great to completely disable the flash writing/reading routines within the ethernut.