[Mark McLeod]

  if(Get_ADC_Result_Count())
  {
    Process_Gyro_Data();
 
    Reset_ADC_Result_Count();
  }

should be called all the time, in autonomous mode or not.

If you follow the default style then the code above would be in Process_Data_From_Local_IO() and you'd need to add a call to Process_Data_From_Local_IO() within the User_Autonomous_Code() autonomous_mode loop (but outside the 26.2ms slow loop).