Index: firmware/App/Modes/FlushPermeate.c
===================================================================
diff -u -r410afd26b3ae5e372310c696c82f58c59235e10d -r8d272582cbd2cb5fc0c6af0fead2867ce02658b0
--- firmware/App/Modes/FlushPermeate.c	(.../FlushPermeate.c)	(revision 410afd26b3ae5e372310c696c82f58c59235e10d)
+++ firmware/App/Modes/FlushPermeate.c	(.../FlushPermeate.c)	(revision 8d272582cbd2cb5fc0c6af0fead2867ce02658b0)
@@ -137,6 +137,12 @@
 {
     FP_PERM_FLUSH_STATE_T state = PERM_FLUSH_IN_PROGRESS;
 
+    if ( TRUE == doesAlarmStatusIndicateStop() )
+    {
+        setPermeateFlushTransition( PERM_FLUSH_PAUSED );
+        state = PERM_FLUSH_PAUSED;
+    }
+
     if( TRUE == didTimeout( permeateFlushTimer, getPermeateFlushTimeout() ) )
     {
         F32 p18conductivity = getFilteredConductivity( P18_COND );
@@ -176,9 +182,6 @@
     if ( TRUE == pendingStartPermeateFlushRequest )
     {
         isFlushComplete = FALSE;
-        pendingStartPermeateFlushRequest = FALSE;
-        permeateFlushTimer = getMSTimerCount();
-        permeateFlushAlarmTimer = getMSTimerCount();
         setPermeateFlushTransition( PERM_FLUSH_IN_PROGRESS );
         state = PERM_FLUSH_IN_PROGRESS;
     }
@@ -207,10 +210,15 @@
             setValveState( P34_VALV, VALVE_STATE_CLOSED );
             setValveState( P37_VALV, VALVE_STATE_CLOSED );
             setValveState( P39_VALV, VALVE_STATE_OPEN );
+
+            if ( TRUE == isBoostPumpInstalled() )
+            {
+                setBoostPumpTargetPressure( PERMEATE_FLUSH_BOOST_PUMP_TGT_PSI );
+            }
             setROPumpTargetPressure( PERMEATE_FLUSH_RO_PUMP_TGT_PSI );
-            setBoostPumpTargetPressure( PERMEATE_FLUSH_BOOST_PUMP_TGT_PSI );
             permeateFlushTimer = getMSTimerCount();
             permeateFlushAlarmTimer = getMSTimerCount();
+            pendingStartPermeateFlushRequest = FALSE;
             break;
 
         case PERM_FLUSH_PAUSED:
@@ -225,7 +233,11 @@
                 setValveState( P34_VALV, VALVE_STATE_CLOSED );
                 setValveState( P37_VALV, VALVE_STATE_CLOSED );
                 setValveState( P39_VALV, VALVE_STATE_CLOSED );
-                signalBoostPumpHardStop();
+
+                if ( TRUE == isBoostPumpInstalled() )
+                {
+                    signalBoostPumpHardStop();
+                }
                 signalROPumpHardStop();
             }
             break;