Oh, and I should mention that the board also has a 328P microcontroller on it. This little guy is designed to communicate via newsoftserial with the bigger Atmel processor. The only other connection between the chips is a shared reset connection. Other than that, they are completely separate. What I do notice though is that as the Bootloader for the 1284P is uploaded, the sck-activity light for the 328P stops blinking. That said, I doubt this is the issue since I was able to upload the bootloader for the 328P just fine.