I built one for a friend and had a hell of time getting my firmware on it. I finally found an option that worked, but I honestly cannot remember which route I took. Although, I do remember that trying to load it with Atmel Flip and that screwed a lot of stuff up. Please don't try to use Flip on this board, as it will cause headaches

When you load firmware and it doesn't "take," it is most likely that there is an error, making it incompatible.
There is a file in the same folder as the firmware flashing .bat that will erase the chip, do that for starters.
I ended up using easyAVR (yes, but do NOT us Flip to push it ) to generate the firmware file that I dragged onto the .bat and that worked the first time. The trouble is that you don't get quite as many options as the default firmware for LEDs.