There was another thread recently where someone was having trouble installing the bootloader on a Mega2560. In the end I suggested getting the AVRISP MkII from Atmel (or some distributor) because that is designed by Atmel for their processors. Then make up an SPI header using the standard (6) pins and you can plug it in and upload the Mega bootloader. I don't know if the 1280 will be any better, I suspect some programmers don't go over 64 Kb properly.