Another issue you can have with S3D is that, even if you delete the temperature controller in the process, S3D will add one back auto-magically.
If you are setting the temp in S3D and it will not hold, try turning the fan down as Kyle suggested. If you are setting your temp manually and it is running at some other temp, try adding ; [extruder0_temperature] to the beginning of your starting gcode in the S3D process you are using. That will make S3D ignore the temperature controller when it generates the gcode for your print.