I've done through the process to upload a new bootloader by using AVR studio 6 + avrisp2 (known as avr isp mkII), but it return no respond to Rx and Tx light to flash when my sample sketch upload on it until no end stop in process uploading.
but I still tried using my another fine Duecimilia board by erase and test it before I test it again by upload same atmega328P type bootloader and to verify it, then is working back to able upload with sketch.
I confirmed that aVR studio 6 + avrisp2 is fine to be able to upload firmware\bootloader into arduino any board flash memory.