I think the problem is that RobotC didn't add in the necessary pragmas to have controllers on the ports S1, and S4.
Code:
#pragma config(Hubs, S1, HTMotor, HTMotor, none, none)
#pragma config(Hubs, S4, HTMotor, HTMotor, HTServo, none)
#pragma config(Sensor, S1, , sensorI2CMuxController)
#pragma config(Sensor, S2, gyro, sensorI2CHiTechnicGyro)
#pragma config(Sensor, S3, HTSMUX, sensorI2CCustom)
#pragma config(Sensor, S4, , sensorI2CMuxController)
#pragma config(Motor, motorA, bristle, tmotorNXT, PIDControl, encoder)
#pragma config(Motor, mtr_S1_C1_1, liftLeft, tmotorTetrix, openLoop, reversed)
#pragma config(Motor, mtr_S1_C1_2, backLeft, tmotorTetrix, openLoop, reversed, encoder)
#pragma config(Motor, mtr_S1_C2_1, frontLeft, tmotorTetrix, openLoop, reversed, encoder)
#pragma config(Motor, mtr_S1_C2_2, flagRaiser, tmotorTetrix, openLoop)
#pragma config(Motor, mtr_S4_C1_1, liftRight, tmotorTetrix, openLoop, reversed, encoder)
#pragma config(Motor, mtr_S4_C1_2, frontRight, tmotorTetrix, openLoop)
#pragma config(Motor, mtr_S4_C2_1, backRight, tmotorTetrix, openLoop, encoder)
#pragma config(Motor, mtr_S4_C2_2, dropper, tmotorTetrix, openLoop)
#pragma config(Servo, srvo_S4_C3_1, ploop, tServoStandard)
#pragma config(Servo, srvo_S4_C3_2, servo2, tServoNone)
#pragma config(Servo, srvo_S4_C3_3, servo3, tServoNone)
#pragma config(Servo, srvo_S4_C3_4, servo4, tServoNone)
#pragma config(Servo, srvo_S4_C3_5, servo5, tServoNone)
#pragma config(Servo, srvo_S4_C3_6, servo6, tServoNone)
//*!!Code automatically generated by 'ROBOTC' configuration wizard !!*//