Since I'm quite able to upload new code to a standard ARDUINO MEGA board without any problems, it seems to me that the computer communicates quite well with a standard ARDUINO board.
In this case when I'm trying to load the bootloader to a "fresh" ATMEGA328, using an ATMEL AVRISPmkII programmer, I'm not sure. The AVR Studio is installed OK, and the driver routine for the programmer is installed. My computer is running Microsoft XP, and it indicates that the driver routine is there.
Is it possible that the Arduino software somehow does not find the driver routine?