Stand-alone flash programmer won't

I can program my Cyclone III from a PC running the full Quartus/NIOS toolset but could not get a Stand-Alone programmer to work.

I've set up Quartus v10 Programmer (programs .SOF file correctly) and copied the files as Appendix C of NiosII Flash Programmer User Guide (Feb 2010) and it appears to work - erase certainly does but the new code is not written.

Discovered the file which controls the IDE Flash Programmer (..\script\flash_programmer.sh) and there are two files generated and programmed. If I program these files one after the other from the CMD line, it all works fine.

I have no idea why there are two files, though, but the problem is solved.