Index: firmware/App/Controllers/ROPump.c
===================================================================
diff -u -r376dfac415321b3d85405e5ef16c48f2118f0f20 -rb576eac158a7bcffd16012dcd5d737e7df4f61d9
--- firmware/App/Controllers/ROPump.c	(.../ROPump.c)	(revision 376dfac415321b3d85405e5ef16c48f2118f0f20)
+++ firmware/App/Controllers/ROPump.c	(.../ROPump.c)	(revision b576eac158a7bcffd16012dcd5d737e7df4f61d9)
@@ -59,15 +59,14 @@
 #define ROP_FLOW_TO_PWM(flow)                   ( ROP_FLOW_TO_PWM_SLOPE * log(flow) + ROP_FLOW_TO_PWM_INTERCEPT )                                        ///< PWM line equation for flow converted to percentage.
 
 #define FP_FLOW_RATE_BELOW_TARGET_TIMEOUT_MS        ( 10 * MS_PER_SECOND )                                              ///< Timeout for flow rate below 75% of target flow rate
-#define FP_FLOW_RATE_BELOW_TARGET_CLEAR_MS          ( 10 * MS_PER_SECOND )                                              ///< Clear timeout for flow rate below target flow rate 
+#define FP_FLOW_RATE_BELOW_TARGET_CLEAR_MS          ( 10 * MS_PER_SECOND )                                              ///< Clear timeout for flow rate below target flow rate
+#define PERMEATE_FLOW_LOW_OUT_OF_RANGE_EXEMPT_MS    ( 10 * MS_PER_SECOND )                                              ///< Permeate flow low alarm exempt for 10 seconds after starting from Off
 
 // ********** private data **********
 
 static RO_PUMP_STATE_T roPumpState;                                                                 ///< Current state of pump controller state machine.
-static RO_PUMP_STATE_T prevROPumpState;                                                             ///< Previous state of RO pump controller state machine.
 static BOOL isROPumpOn;                                                                             ///< Flag indicating whether pump is currently running.
 static BOOL stopPumpRequest;                                                                        ///< Flag indicating pump stop is requested.
-static BOOL exemptLowFlowAlarm;                                                                     ///< Flag indicating whether to exempt low permeate flow alarm.
 static U32 roPumpDataPublicationTimerCounter;                                                       ///< Used to schedule RO pump data publication to CAN bus.
 static OVERRIDE_U32_T roPumpDataPublishInterval;                                                    ///< Interval (in ms) at which to publish boost pump data to CAN bus.
 static U32 roControlTimerCounter;                                                                   ///< Determines when to perform control on RO pump.
@@ -76,7 +75,7 @@
 static F32 roPumpDutyCyclePctSet;                                                                   ///< Currently set RO pump PWM duty cycle.
 static OVERRIDE_F32_T roPumpOpenLoopTargetDutyCycle;                                                ///< Target RO pump open loop PWM.
 static BOOL roPumpStartControl;                                                                     ///< boolean to determine when closed loop flow control starts
-static U32 lowFlowExemptTimer;                                                                      ///< Timer to exempt low flow rate alarm
+static U32 timeSinceStart;                                                                          ///< Time when RO pump is started from off state.
 
 // ********** private function prototypes **********
 
@@ -85,6 +84,7 @@
 static RO_PUMP_STATE_T handleROPumpControlToTargetPressureState( void );
 static RO_PUMP_STATE_T handleROPumpOpenLoopState( void );
 
+static U32 getROPumpLowFlowExemptTimer( void );
 static F32 roPumpPresToPWM( F32 targetPressure );
 static F32 roPumpFlowToPWM( U32 targetFlow );
 static void stopROPump( void );
@@ -93,10 +93,7 @@
 /*********************************************************************//**
  * @brief
  * The initROPump function initializes the RO Pump module.
- * @details \b Inputs: roPumpState, prevROPumpState, roPumpControlMode, isROPumpOn,
- * stopPumpRequest, roControlTimerCounter, roPumpDutyCyclePctSet,
- * roPumpOpenLoopTargetDutyCycle, roPumpDataPublicationTimerCounter, roPumpDataPublishInterval,
- * targetROPumpFlowRate, targetROPumpPressure, exemptLowFlowAlarm, lowFlowExemptTimer
+ * @details \b Inputs: none
  * @details \b Outputs: RO Pump controller unit initialized
  * @return none
  *************************************************************************/
@@ -113,10 +110,8 @@
                             MIN_FLUID_PUMP_DUTY_CYCLE_PCT, MAX_FLUID_PUMP_DUTY_CYCLE_PCT, FALSE, 0 );
 
     roPumpState                                 = RO_PUMP_OFF_STATE;
-    prevROPumpState                             = RO_PUMP_OFF_STATE;
     isROPumpOn                                  = FALSE;
     stopPumpRequest                             = FALSE;
-    exemptLowFlowAlarm                          = TRUE;
     roControlTimerCounter                       = 0;
     roPumpDutyCyclePctSet                       = 0.0F;
     roPumpStartControl                          = FALSE;
@@ -137,7 +132,7 @@
     roPumpOpenLoopTargetDutyCycle.ovData        = 0.0;
     roPumpOpenLoopTargetDutyCycle.ovInitData    = 0.0;
     roPumpOpenLoopTargetDutyCycle.override      = OVERRIDE_RESET;
-    lowFlowExemptTimer                          = 0;
+    timeSinceStart                              = 0;
 
     stopROPump();
 }
@@ -179,15 +174,6 @@
             break;
     }
 
-    if ( prevROPumpState == RO_PUMP_OFF_STATE )
-    {
-        exemptLowFlowAlarm = TRUE;
-    }
-    else
-    {
-        exemptLowFlowAlarm = FALSE;
-    }
-    prevROPumpState = roPumpState;
     // Publish RO pump data on interval
     publishROPumpData();
 }
@@ -204,7 +190,7 @@
 {
     RO_PUMP_STATE_T state   = RO_PUMP_OFF_STATE;
     isROPumpOn              = FALSE;
-    lowFlowExemptTimer      = 0;
+    timeSinceStart          = 0;
 
     // If there is a target flow set, transition to the PI controller and control to flow
     if ( getTargetROPumpFlowRateMLPM() > 0 )
@@ -215,7 +201,6 @@
         resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, roPumpDutyCyclePctSet, 0.0F );
         setFluidPumpPctToPWMDutyCycle( P12_PUMP, roPumpDutyCyclePctSet );
         roPumpStartControl = FALSE;
-        lowFlowExemptTimer = getMSTimerCount();
         state = RO_PUMP_CONTROL_TO_TARGET_FLOW_STATE;
     }
     // If there is a target pressure set, transition to the PI controller and control to pressure.
@@ -226,7 +211,6 @@
         roPumpDutyCyclePctSet = roPumpPresToPWM( getTargetROPumpPressure() );
         resetPIController( PI_CONTROLLER_ID_RO_PUMP_PRES, roPumpDutyCyclePctSet, 0.0F );
         setFluidPumpPctToPWMDutyCycle( P12_PUMP, roPumpDutyCyclePctSet );
-        lowFlowExemptTimer = getMSTimerCount();
         state = RO_PUMP_CONTROL_TO_TARGET_PRESSURE_STATE;
     }
     // If the target duty cycle is greater than zero (minimum is 10%) and the mode has been set to open
@@ -236,10 +220,14 @@
         roPumpDutyCyclePctSet = getTargetROPumpDutyCyclePCT();
         setFluidPumpPctToPWMDutyCycle( P12_PUMP, roPumpDutyCyclePctSet );
         isROPumpOn = TRUE;
-        lowFlowExemptTimer = getMSTimerCount();
         state = RO_PUMP_OPEN_LOOP_STATE;
     }
 
+    if ( state != RO_PUMP_OFF_STATE )
+    {
+        timeSinceStart = getMSTimerCount();
+    }
+
     return state;
 }
 
@@ -618,28 +606,35 @@
 
 /*********************************************************************//**
  * @brief
- * The getROPumpLowFlowExemptTimer function gets the timer when RO pump
- * starts from Off state.
+ * The exemptROPumpLowFlowAlarm function gets the flag whether or not
+ * to exempt the low flow alarm.
  * @details \b Inputs: none
  * @details \b Outputs: none
- * @return the timer when RO pump started from Off state (in ms).
+ * @return the flag whether or not to exempt low flow alarm.
  *************************************************************************/
-U32 getROPumpLowFlowExemptTimer( void )
+BOOL exemptROPumpLowFlowAlarm( void )
 {
-    return lowFlowExemptTimer;
+    BOOL result = FALSE;
+
+    if ( ( roPumpState == RO_PUMP_CONTROL_TO_TARGET_FLOW_STATE ) && ( FALSE == didTimeout( getROPumpLowFlowExemptTimer(), PERMEATE_FLOW_LOW_OUT_OF_RANGE_EXEMPT_MS ) ) )
+    {
+        result = TRUE;
+    }
+
+    return result;
 }
 
 /*********************************************************************//**
  * @brief
- * The getROPumpLowFlowExemptFlag function gets the flag whether or not
- * to exempt the low flow alarm.
+ * The getROPumpLowFlowExemptTimer function gets the timer when RO pump
+ * starts from Off state.
  * @details \b Inputs: none
  * @details \b Outputs: none
- * @return the flag whether or not to exempt low flow alarm (in mL/min).
+ * @return the timer when RO pump started from Off state (in ms).
  *************************************************************************/
-BOOL getROPumpLowFlowExemptFlag( void )
+static U32 getROPumpLowFlowExemptTimer( void )
 {
-    return exemptLowFlowAlarm;
+    return timeSinceStart;
 }
 
 /*********************************************************************//**