It looks like I can read from both the Flash and CS8900 but cannot write to them.
Like I said before I have checked with a scope to see if there is signal and it looks OK. Will quickly try again with known working Flash code.
I have thought that NIOS2 jumbled the address or data lines up. Garbage put in a certain way will come out exactly the same way on RAM. Flash however needs a specific code to write and erase data. But the data written by NIOS1 is the same as read by NIOS2, meaning that the address and data lines are correct.
Will check and come back
VictorS