Index: firmware/App/Controllers/ROPump.c
===================================================================
diff -u -re706d20db89e55c51ba0c6f5c33842e117f965ab -rbb1b5860c4a87ee17537ae9f6ca690a4d74bc925
--- firmware/App/Controllers/ROPump.c	(.../ROPump.c)	(revision e706d20db89e55c51ba0c6f5c33842e117f965ab)
+++ firmware/App/Controllers/ROPump.c	(.../ROPump.c)	(revision bb1b5860c4a87ee17537ae9f6ca690a4d74bc925)
@@ -17,6 +17,7 @@
 #include <math.h>           // for log()
 
 #include "Flow.h"
+#include "FPOperationModes.h"
 //#include "NVDataMgmt.h"
 #include "Messaging.h"
 #include "MessageSupport.h"
@@ -40,7 +41,7 @@
 #define ROP_CONTROL_INTERVAL                        ( MS_PER_SECOND / TASK_GENERAL_INTERVAL )                           ///< Interval (ms/task time) at which the RO pump is controlled.
 
 #define ROP_FLOW_CONTROL_P_COEFFICIENT              0.000065F                                                           ///< P term for RO pump flow control.
-#define ROP_FLOW_CONTROL_I_COEFFICIENT              0.00020F                                                            ///< I term for RO pump flow control.
+#define ROP_FLOW_CONTROL_I_COEFFICIENT              0.00022F                                                            ///< I term for RO pump flow control.
 #define ROP_MIN_FLOW_TO_CONTROL_PCT                 0.75F
 #define ROP_PRESSURE_CONTROL_P_COEFFICIENT          0.15F                                                               ///< P term for RO pump pressure control.
 #define ROP_PRESSURE_CONTROL_I_COEFFICIENT          0.65F                                                               ///< I term for RO pump pressure control.
@@ -241,7 +242,14 @@
     if ( getTargetROPumpFlowRateMLPM() > 0 )
     {
         ///transition to closed loop
-        roPumpDutyCyclePctSet = roPumpFlowToPWM( getTargetROPumpFlowRateMLPM() );
+        if ( getCurrentOperationMode() == FP_MODE_GENP )
+        {
+            roPumpDutyCyclePctSet =  getCurrentROPumpDutyCyclePCT();
+        }
+        else
+        {
+            roPumpDutyCyclePctSet = roPumpFlowToPWM( getTargetROPumpFlowRateMLPM() );
+        }
         resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, roPumpDutyCyclePctSet, 0.0F );
         state = RO_PUMP_CONTROL_TO_TARGET_FLOW_STATE;
     }
Index: firmware/App/Modes/ModeGenPermeate.c
===================================================================
diff -u -r764e0e8c7a889f72a9b6bdced9ef08a09d72b36e -rbb1b5860c4a87ee17537ae9f6ca690a4d74bc925
--- firmware/App/Modes/ModeGenPermeate.c	(.../ModeGenPermeate.c)	(revision 764e0e8c7a889f72a9b6bdced9ef08a09d72b36e)
+++ firmware/App/Modes/ModeGenPermeate.c	(.../ModeGenPermeate.c)	(revision bb1b5860c4a87ee17537ae9f6ca690a4d74bc925)
@@ -45,6 +45,7 @@
 #define PUMP_REST_TIMEOUT_MS                       ( 3 * MS_PER_SECOND )                        ///< Verify Water timer ( in ms )
 #define RO_REJECTION_WAIT_TIME_MS                  ( 8 * MS_PER_SECOND )                        ///< Verify Water timer ( in ms )
 #define MIN_RO_REJECTION_RATIO_PCT                 90.0F                                        ///< Minimum RO rejection ration in percentage
+#define MIN_SAMPLES_NEEDED_FOR_DUTY_CYCLE_AVG      10                                           ///< Minimum number for samples needed for calculating the average duty cycle
 
 // ********** private data **********
 
@@ -215,11 +216,9 @@
 {
     FP_GENP_MODE_STATE_T state = FP_GENP_TANK_FILL_STATE;
     PERMEATE_TANK_STATE_T permemeateTankState = getPermeateTankState();
-    F32 initDutyCycle = isFillAvgValid ? prevFillAvgDutyCycle : getCurrentROPumpDutyCyclePCT();
     if ( TRUE == didTimeout( timeInState, PUMP_REST_TIMEOUT_MS ) && stateTransitioned == TRUE )
     {
         stateTransitioned = FALSE;
-        resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, initDutyCycle, 0.0F );
         setROPumpTargetFlowRateMLPM( GEN_PERMEATE_RO_PUMP_TGT_ML, TRUE );
     }
     // Wait for RO rejection to stabilize after transition from full to fill + RO Rejection moving average duration
@@ -250,11 +249,9 @@
 static FP_GENP_MODE_STATE_T handleGenPTankFullState( void )
 {
     FP_GENP_MODE_STATE_T state = FP_GENP_TANK_FULL_STATE;
-    F32 initDutyCycle = isFullAvgValid ? prevFullAvgDutyCycle : getCurrentROPumpDutyCyclePCT();
     if ( TRUE == didTimeout( timeInState, PUMP_REST_TIMEOUT_MS ) && stateTransitioned == TRUE )
     {
         stateTransitioned = FALSE;
-        resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, initDutyCycle, 0.0F );
         setROPumpTargetFlowRateMLPM( GEN_PERMEATE_RO_PUMP_TGT_ML, TRUE );
     }
     PERMEATE_TANK_STATE_T permemeateTankState = getPermeateTankState();
@@ -303,14 +300,14 @@
  *************************************************************************/
 static void calculateDutyCycleAvg( FP_GENP_MODE_STATE_T state )
 {
-    if ( state == FP_GENP_TANK_FILL_STATE && fillDutyCount > 0)
+    if ( state == FP_GENP_TANK_FILL_STATE && fillDutyCount > MIN_SAMPLES_NEEDED_FOR_DUTY_CYCLE_AVG)
     {
         prevFillAvgDutyCycle = fillDutySum / (F32)fillDutyCount;
         isFillAvgValid       = TRUE;
         fillDutySum          = 0.0F;
         fillDutyCount        = 0;
     }
-    else if ( state == FP_GENP_TANK_FULL_STATE && fullDutyCount > 0 )
+    else if ( state == FP_GENP_TANK_FULL_STATE && fullDutyCount > MIN_SAMPLES_NEEDED_FOR_DUTY_CYCLE_AVG )
     {
         prevFullAvgDutyCycle = fullDutySum / (F32)fullDutyCount;
         isFullAvgValid       = TRUE;