Index: firmware/App/Controllers/BoostPump.c
===================================================================
diff -u -r5e5ece62c01bc4576acd936fb4b200e8a336f2c2 -r2506bb824f04982d4cf6ad3d81853f863b2f9c11
--- firmware/App/Controllers/BoostPump.c	(.../BoostPump.c)	(revision 5e5ece62c01bc4576acd936fb4b200e8a336f2c2)
+++ firmware/App/Controllers/BoostPump.c	(.../BoostPump.c)	(revision 2506bb824f04982d4cf6ad3d81853f863b2f9c11)
@@ -247,7 +247,7 @@
     // If there is a target pressure set, transition to the PI controller and control to pressure.
     if ( ( getTargetBoostPumpPressure() > 0.0F ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == boostPumpControlMode ) )
     {
-        //transition to closed loop
+        // Transition to closed loop
         resetPIController( PI_CONTROLLER_ID_BOOST_PUMP_PRES, boostPumpDutyCyclePctSet, 0.0F );
         state = BOOST_PUMP_CONTROL_TO_TARGET_PRESSURE_STATE;
     }
@@ -275,11 +275,24 @@
 {
     BOOST_PUMP_STATE_T state = BOOST_PUMP_CONTROL_TO_TARGET_FLOW_STATE;
 
+    // Check if need to switch control modes
+    if ( getTargetROPumpPressure() > 0.0F && ( PUMP_CONTROL_MODE_CLOSED_LOOP == boostPumpControlMode ) )
+    {
+        // Transition to target pressure
+        resetPIController( PI_CONTROLLER_ID_BOOST_PUMP_PRES, boostPumpDutyCyclePctSet, 0 );
+        state = BOOST_PUMP_CONTROL_TO_TARGET_PRESSURE_STATE;
+    }
+    else if ( boostPumpOpenLoopTargetDutyCycle > 0.0F && ( PUMP_CONTROL_MODE_OPEN_LOOP == boostPumpControlMode ) )
+    {
+        setFluidPumpPctToPWMDutyCycle( P40_PUMP, boostPumpOpenLoopTargetDutyCycle );
+        boostPumpDutyCyclePctSet = boostPumpOpenLoopTargetDutyCycle;
+        state = BOOST_PUMP_OPEN_LOOP_STATE;
+    }
     // Control at set interval
-    if ( ( ++boostControlTimerCounter >= BOOST_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == boostPumpControlMode ) )
+    else if ( ( ++boostControlTimerCounter >= BOOST_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == boostPumpControlMode ) )
     {
         boostPumpDutyCyclePctSet = runPIController( PI_CONTROLLER_ID_BOOST_PUMP_FLOW, getTargetBoostPumpFlowRateLPM(), getFlowRate( P7_FLOW ) );
-        setFluidPumpPctToPWMDutyCycle( P12_PUMP, boostPumpDutyCyclePctSet );
+        setFluidPumpPctToPWMDutyCycle( P40_PUMP, boostPumpDutyCyclePctSet );
         boostControlTimerCounter = 0;
     }
 
@@ -298,11 +311,23 @@
 {
     BOOST_PUMP_STATE_T state = BOOST_PUMP_CONTROL_TO_TARGET_PRESSURE_STATE;
 
+    if ( ( getTargetBoostPumpFlowRateLPM() > 0.0F ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == boostPumpControlMode ) )
+    {
+        ///transition to target flow
+        resetPIController( PI_CONTROLLER_ID_BOOST_PUMP_FLOW, boostPumpDutyCyclePctSet, 0.0F );
+        state = BOOST_PUMP_CONTROL_TO_TARGET_FLOW_STATE;
+    }
+    else if ( boostPumpOpenLoopTargetDutyCycle > 0.0F && ( PUMP_CONTROL_MODE_OPEN_LOOP == boostPumpControlMode ) )
+    {
+        setFluidPumpPctToPWMDutyCycle( P40_PUMP, boostPumpOpenLoopTargetDutyCycle );
+        boostPumpDutyCyclePctSet = boostPumpOpenLoopTargetDutyCycle;
+        state = BOOST_PUMP_OPEN_LOOP_STATE;
+    }
     // Control at set interval
-    if ( ( ++boostControlTimerCounter >= BOOST_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == boostPumpControlMode ) )
+    else if ( ( ++boostControlTimerCounter >= BOOST_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == boostPumpControlMode ) )
     {
         boostPumpDutyCyclePctSet = runPIController( PI_CONTROLLER_ID_BOOST_PUMP_PRES, getTargetBoostPumpPressure(), getFilteredPressure( M3_PRES ) );
-        setFluidPumpPctToPWMDutyCycle( P12_PUMP, boostPumpDutyCyclePctSet );
+        setFluidPumpPctToPWMDutyCycle( P40_PUMP, boostPumpDutyCyclePctSet );
         boostControlTimerCounter = 0;
     }
 
@@ -418,7 +443,7 @@
         status                           = TRUE;
 
         // Set the new duty cycle of the pump
-        setFluidPumpPctToPWMDutyCycle( P12_PUMP, boostPumpOpenLoopTargetDutyCycle );
+        setFluidPumpPctToPWMDutyCycle( P40_PUMP, boostPumpOpenLoopTargetDutyCycle );
         // Clear previous target data
         if ( getTargetBoostPumpFlowRateLPM() > 0.0F )
         {
Index: firmware/App/Controllers/ROPump.c
===================================================================
diff -u -r5e5ece62c01bc4576acd936fb4b200e8a336f2c2 -r2506bb824f04982d4cf6ad3d81853f863b2f9c11
--- firmware/App/Controllers/ROPump.c	(.../ROPump.c)	(revision 5e5ece62c01bc4576acd936fb4b200e8a336f2c2)
+++ firmware/App/Controllers/ROPump.c	(.../ROPump.c)	(revision 2506bb824f04982d4cf6ad3d81853f863b2f9c11)
@@ -274,8 +274,21 @@
 {
     RO_PUMP_STATE_T state = RO_PUMP_CONTROL_TO_TARGET_FLOW_STATE;
 
+    // Check if need to switch control modes
+    if ( getTargetROPumpPressure() > 0.0F && ( PUMP_CONTROL_MODE_CLOSED_LOOP == roPumpControlMode ) )
+    {
+        // Transition to target pressure
+        resetPIController( PI_CONTROLLER_ID_RO_PUMP_PRES, roPumpDutyCyclePctSet, 0 );
+        state = RO_PUMP_CONTROL_TO_TARGET_PRESSURE_STATE;
+    }
+    else if ( roPumpOpenLoopTargetDutyCycle > 0.0F && ( PUMP_CONTROL_MODE_OPEN_LOOP == roPumpControlMode ) )
+    {
+        setFluidPumpPctToPWMDutyCycle( P12_PUMP, roPumpOpenLoopTargetDutyCycle );
+        roPumpDutyCyclePctSet = roPumpOpenLoopTargetDutyCycle;
+        state = RO_PUMP_OPEN_LOOP_STATE;
+    }
     // Control at set interval
-    if ( ( ++roControlTimerCounter >= ROP_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == roPumpControlMode ) )
+    else if ( ( ++roControlTimerCounter >= ROP_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == roPumpControlMode ) )
     {
         roPumpDutyCyclePctSet = runPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, getTargetROPumpFlowRateLPM(), getFlowRate( P16_FLOW ) );
         setFluidPumpPctToPWMDutyCycle( P12_PUMP, roPumpDutyCyclePctSet );
@@ -297,8 +310,20 @@
 {
     RO_PUMP_STATE_T state = RO_PUMP_CONTROL_TO_TARGET_PRESSURE_STATE;
 
+    if ( getTargetROPumpFlowRateLPM() > 0.0F && ( PUMP_CONTROL_MODE_CLOSED_LOOP == roPumpControlMode ) )
+    {
+        // Transition to target flow
+        resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, roPumpDutyCyclePctSet, 0 );
+        state = RO_PUMP_CONTROL_TO_TARGET_FLOW_STATE;
+    }
+    else if ( roPumpOpenLoopTargetDutyCycle > 0.0F && ( PUMP_CONTROL_MODE_OPEN_LOOP == roPumpControlMode ) )
+    {
+        setFluidPumpPctToPWMDutyCycle( P12_PUMP, roPumpOpenLoopTargetDutyCycle );
+        roPumpDutyCyclePctSet = roPumpOpenLoopTargetDutyCycle;
+        state = RO_PUMP_OPEN_LOOP_STATE;
+    }
     // Control at set interval
-    if ( ( ++roControlTimerCounter >= ROP_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == roPumpControlMode ) )
+    else if ( ( ++roControlTimerCounter >= ROP_CONTROL_INTERVAL ) && ( PUMP_CONTROL_MODE_CLOSED_LOOP == roPumpControlMode ) )
     {
         roPumpDutyCyclePctSet = runPIController( PI_CONTROLLER_ID_RO_PUMP_PRES, getTargetROPumpPressure(), getFilteredPressure( P17_PRES ) );
         setFluidPumpPctToPWMDutyCycle( P12_PUMP, roPumpDutyCyclePctSet );
@@ -520,10 +545,10 @@
         resetPIController( PI_CONTROLLER_ID_RO_PUMP_PRES, MIN_FLUID_PUMP_DUTY_CYCLE_PCT, 0.0F );
     }
 
-    roPumpState = RO_PUMP_OFF_STATE;
     roPumpDutyCyclePctSet = 0.0F;
     roControlTimerCounter = 0;
     roPumpOpenLoopTargetDutyCycle = 0;
+    stopPumpRequest = TRUE;
     stopROPump();
 }
 
@@ -537,7 +562,6 @@
 static void stopROPump( void )
 {
     isROPumpOn = FALSE;
-    roPumpDutyCyclePctSet = 0.0F;
     // Set the new duty cycle of the pump
     setFluidPumpPWMDutyCycle( P12_PUMP, 0 );
 }