I had a similar problem. Specifically, I built both my motherboard and the extruder board. I've burned the bootloader on both (without issue, as far as I can tell), and I can push code to the extruder controller with my usb bub (http://moderndevice.com/connect.shtml).
I cannot, however, push code to the motherboard. I get a 'no response' error from avrdude. I've tried this with my USBtinyISP plugged in to help power the board (with the jumper set), and without the icsp. I've double checked connections and tried re-burning the bootloader, but to no avail.
My current plan is to borrow a different programming adapter from a friend and try that, although do not expect this to make a difference. I would be very happy to hear suggestions for other debugging I can do.
