Thanks Daixiwen
I should have said that i have tried the following programming procedure:
using quartus programmer Uploaded the .sof with JTAG
The hardware (and software? maybe stays on from last time the elf was loaded) appear to work fine at this stage
with power still on i then......
using nios flash programmer Uploaded the .sof (sof2flash) with JTAG
The hardware is now non volatile and works after power cycle but fails to run software
Uploaded the .elf (elf2flash) with JTAG
The hardware software now work on soft reset but after a power cycle it appears that the hardware is gone and with logic elements not generating expected activity on the boards LED's and consequently no CPU activity.
Jockeyjim