Last year, when I was testing my autonomous mode bin-hunting algorithm (servos + reflection sensors), there was still a bug in it. Whenever the robot didn't have a 'lock' on something in front of it (like a bin), it would go straight backwards. So, it had a lock on a bin, but then it lost it, and went from full forward to full reverse, and one of the motors started smoking. We ended up having to replace that motor, as it was never as strong as it used to be after that. I recommend you start talking to FIRST about getting yourself a new motor.
And then I never got a chance to test my (fixed) autonomous mode, we never were sure that it worked, so we never had an autonomous mode.
