Would you be willing to post your code (including the #pragma statements at the top of the program) using the [code] tags? This way we can check and make sure the motor controllers are set up properly.
Also, double check to make sure that the cables from the NXT are daisy chained correctly and that the controllers are configured correctly in the Motors and Sensors Setup window (found in the Robot menu in ROBOTC). We have a quick setup guide on our wiki
that can show you how to do this.
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