Jessey,
Here is a small refinement to your IF-THEN-ENDIF
Code:
  Temp = Seconds + Minutes + Hours + Seconds_Alarm_Set_Point + _
               Minutes_Alarm_Set_Point + Hours_Alarm_Set_Point
  IF Temp <> 0 THEN  'Not Equal to 0
                     '<- Eliminates the unused ELSE
      IF Start_Stop_Mode = StartTime THEN   
          IF Hours = Hours_Alarm_Set_Point THEN
              IF Minutes = Minutes_Alarm_Set_Point THEN
                  IF Seconds = Seconds_Alarm_Set_Point THEN
                      GOSUB StopTimer
                      LOW Clock_Active_Green_Led : Alarm_Is = On_  
                   ENDIF
              ENDIF    
          ENDIF
     ENDIF
  ENDIF
Steve