That's a very good updated document. I load the hex file and then READ in the QCX software to check the usb was working. I did read about that on AVRDUDE if you read in the firmware form QCX it would overwrite the existing hex file.
I unzipped the hex ZIP file again and loaded that into burner and the QCX got programmed sucessfully.
I think reading in the the firmware from the QCX overwrote the hex file.
Following the exact instruction order on the PDF should work with no problem.