When you burned the bootloader were you on a breadboard with internal or external oscillator (crystal)? Or did you do this 'In Circuit' of the Servo Controller board or via another method/programmer? Did you burn the UNO, Duemilanove bootloader or the breadboard version? When you were loading/burning the bootloader did you look to the messages out put on the serial terminal while the process was ongoing? Were there error messages(?) that you may have missed? Was the programming interface actually able to connect at that time? Did you check for the blinking signal on pin thirteen of the Atmega328P? Did you properly set the Fuses? Too many questions?
The Arduindo bootloader has a blink program built into it that signals pin thirteen to blink an LED on that pin. This is how you can generally tell if it is indeed loaded. Did you check for this? I'm not familiar with the Motor Controller circuitry. Does that board have an LED attached to that pin 13 for verification?
IF - the bootloader is indeed on the chip. How are you connecting to the board? Is it through USB-serial and via the Arduino IDE? Have you adjusted the various files to assure your programming method and setup is reflected within the IDE so that connection/programming for sketches can take place? Some methods use USB from an Atmega chip and not FTDI's USB to Serial so the configuration has to work within Arduino's IDE.
Anyway - You probably have gone over all that I suggested but maybe it jogged some thoughts. Now, you can start checking. Oh, don't hope you just found a guru. I very recently just happened to build something from chip up and have struggled through some stuff. I, also, am new to all this so, I've learned what to ask about. I can point and suggest. You will have to search and look for what hints you may get - from me anyway. Good luck and have fun!
