Index: firmware/App/Controllers/AirPump.c
===================================================================
diff -u -rda7e8c1b71db9273f83e9d0ba7d20e74e758a8ad -r33c3a81272ce8c9bae64ae20537e9be45b11edd0
--- firmware/App/Controllers/AirPump.c	(.../AirPump.c)	(revision da7e8c1b71db9273f83e9d0ba7d20e74e758a8ad)
+++ firmware/App/Controllers/AirPump.c	(.../AirPump.c)	(revision 33c3a81272ce8c9bae64ae20537e9be45b11edd0)
@@ -62,6 +62,7 @@
 static void publishAirPumpData( void );
 static void execAirPumpMonitor( void );
 static void setAirPumpMotor( AIR_PUMP_MOTOR_STATE_T state );
+static AIR_PUMP_MOTOR_STATE_T getAirPumpMotorState( void );
 
 /*********************************************************************//**
  * @brief
@@ -185,10 +186,12 @@
 {
     if ( MODE_TREA == getCurrentOperationMode() )
     {
-        if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_HD_AIR_PUMP_TIMEOUT, (BOOL)getAirPumpMotorState() ) )
+        BOOL isAirPumpOn = ( AIR_PUMP_MOTOR_OFF == getAirPumpMotorState() ? FALSE : TRUE );
+
+        if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_HD_AIR_PUMP_TIMEOUT, isAirPumpOn ) )
         {
-            SET_ALARM_WITH_1_U32_DATA( ALARM_ID_HD_AIR_PUMP_TIMEOUT, getAirPumpMotorState() );
-            setAirPumpState(AIR_PUMP_STATE_OFF);
+            SET_ALARM_WITH_1_U32_DATA( ALARM_ID_HD_AIR_PUMP_TIMEOUT, isAirPumpOn );
+            setAirPumpState( AIR_PUMP_STATE_OFF );
         }
     }
 }
Index: firmware/App/Controllers/AirTrap.c
===================================================================
diff -u -rda7e8c1b71db9273f83e9d0ba7d20e74e758a8ad -r33c3a81272ce8c9bae64ae20537e9be45b11edd0
--- firmware/App/Controllers/AirTrap.c	(.../AirTrap.c)	(revision da7e8c1b71db9273f83e9d0ba7d20e74e758a8ad)
+++ firmware/App/Controllers/AirTrap.c	(.../AirTrap.c)	(revision 33c3a81272ce8c9bae64ae20537e9be45b11edd0)
@@ -346,6 +346,7 @@
         pendingStopAirTrapController = FALSE;
         result = AIR_TRAP_MANUAL_CONTROL_STATE;
     }
+
     //Turn on air pump if fluid reaches upper level.
     else if ( AIR_TRAP_LEVEL_FLUID == getAirTrapLevel( AIR_TRAP_LEVEL_SENSOR_UPPER ) )
     {
Index: firmware/App/Controllers/Bubble.c
===================================================================
diff -u -r0a4dcd288d4347b85baaa0b07da568b6add5eac7 -r33c3a81272ce8c9bae64ae20537e9be45b11edd0
--- firmware/App/Controllers/Bubble.c	(.../Bubble.c)	(revision 0a4dcd288d4347b85baaa0b07da568b6add5eac7)
+++ firmware/App/Controllers/Bubble.c	(.../Bubble.c)	(revision 33c3a81272ce8c9bae64ae20537e9be45b11edd0)
@@ -209,6 +209,7 @@
                     {
                         case TREATMENT_BLOOD_PRIME_STATE:
                         case TREATMENT_DIALYSIS_STATE:
+                        case TREATMENT_STOP_STATE:
                         case TREATMENT_END_STATE:
                             activateAlarmNoData( ALARM_ID_HD_VENOUS_BUBBLE_DETECTED );
                             break;
Index: firmware/App/Controllers/PresOccl.c
===================================================================
diff -u -r5d9c5362b537331248dc592e05b6b016267eb6d3 -r33c3a81272ce8c9bae64ae20537e9be45b11edd0
--- firmware/App/Controllers/PresOccl.c	(.../PresOccl.c)	(revision 5d9c5362b537331248dc592e05b6b016267eb6d3)
+++ firmware/App/Controllers/PresOccl.c	(.../PresOccl.c)	(revision 33c3a81272ce8c9bae64ae20537e9be45b11edd0)
@@ -474,7 +474,8 @@
         // Check arterial pressure during treatment mode against either user set limits or fixed max limits depending on treatment state
         if ( ( MODE_TREA == getCurrentOperationMode() ) &&
              ( ( ( TREATMENT_DIALYSIS_STATE == txState ) && ( getDialysisState() != DIALYSIS_SALINE_BOLUS_STATE ) ) ||
-               ( ( TREATMENT_STOP_STATE == txState ) && ( TRUE == isBloodPumpRunning() ) ) ) )
+               ( ( TREATMENT_STOP_STATE == txState ) && ( TRUE == isBloodPumpRunning() ) ) ||
+               ( TREATMENT_BLOOD_PRIME_STATE == txState ) ) )
         {
             F32 artLowLimit  = (F32)getTreatmentParameterS32( TREATMENT_PARAM_ART_PRESSURE_LOW_LIMIT );
             F32 artHighLimit = (F32)getTreatmentParameterS32( TREATMENT_PARAM_ART_PRESSURE_HIGH_LIMIT );
@@ -540,7 +541,8 @@
         // Check venous pressure during treatment mode against either user set limits or fixed max limits depending on treatment state
         if ( ( MODE_TREA == getCurrentOperationMode() ) &&
              ( ( ( TREATMENT_DIALYSIS_STATE == txState ) && ( getDialysisState() != DIALYSIS_SALINE_BOLUS_STATE ) ) ||
-               ( ( TREATMENT_STOP_STATE == txState ) && ( TRUE == isBloodPumpRunning() ) ) ) )
+               ( ( TREATMENT_STOP_STATE == txState ) && ( TRUE == isBloodPumpRunning() ) ) ||
+               ( TREATMENT_BLOOD_PRIME_STATE == txState ) ) )
         {
             F32 venLowLimit  = (F32)getTreatmentParameterS32( TREATMENT_PARAM_VEN_PRESSURE_LOW_LIMIT );
             F32 venHighLimit = (F32)getTreatmentParameterS32( TREATMENT_PARAM_VEN_PRESSURE_HIGH_LIMIT );
Index: firmware/App/Modes/BloodPrime.c
===================================================================
diff -u -r0a4dcd288d4347b85baaa0b07da568b6add5eac7 -r33c3a81272ce8c9bae64ae20537e9be45b11edd0
--- firmware/App/Modes/BloodPrime.c	(.../BloodPrime.c)	(revision 0a4dcd288d4347b85baaa0b07da568b6add5eac7)
+++ firmware/App/Modes/BloodPrime.c	(.../BloodPrime.c)	(revision 33c3a81272ce8c9bae64ae20537e9be45b11edd0)
@@ -37,7 +37,6 @@
 // ********** private definitiions ***********
 
 #define TUBING_BLOOD_PRIME_VOLUME_ML                80.0F                   ///< Target blood prime volume to prime the blood side circuit (in mL).
-#define DEFAULT_BLOOD_PRIME_VOLUME_ML               300.0F                  ///< Default blood prime volume (in mL).
 #define MAX_BLOOD_PRIME_VOLUME_ERROR_ML             60.0F                   ///< Maximum error in total additional blood prime volume (20% of total).
 #define MIN_RAMP_TIME_SEC                           60                      ///< Minimum ramp time for blood prime (in seconds).
 
@@ -94,7 +93,6 @@
     bloodPrimePublishTimerCtr = BLOOD_PRIME_DATA_PUBLISH_INTERVAL - 2;  // setup so publish will occur time after next
     cumulativeBloodPrimeVolume_mL.data = 0.0;
     expectedBloodPrimeVolume_mL = 0.0;
-    bloodPrimeTargetVolume_mL = DEFAULT_BLOOD_PRIME_VOLUME_ML;
     resetBloodPrimeFlags();
 
     bloodPrimeTargetVolume_mL = (F32)TUBING_BLOOD_PRIME_VOLUME_ML + (F32)getDialyzerBloodVolume();
Index: firmware/App/Modes/Dialysis.c
===================================================================
diff -u -r81c902fb595b9fcde229f8898d14e43312969f26 -r33c3a81272ce8c9bae64ae20537e9be45b11edd0
--- firmware/App/Modes/Dialysis.c	(.../Dialysis.c)	(revision 81c902fb595b9fcde229f8898d14e43312969f26)
+++ firmware/App/Modes/Dialysis.c	(.../Dialysis.c)	(revision 33c3a81272ce8c9bae64ae20537e9be45b11edd0)
@@ -128,15 +128,17 @@
 {
     U16 i;
 
-    currentDialysisState = DIALYSIS_START_STATE;
-    currentUFState = UF_START_STATE;
+    currentDialysisState = DIALYSIS_UF_STATE;
+    currentUFState = UF_RUNNING_STATE;
     currentSalineBolusState = SALINE_BOLUS_STATE_IDLE;
 
+    lastUFTimeStamp = getMSTimerCount();
+    uFTimeMS = 0;
+
     refUFVolume = 0.0;
     measUFVolume = 0.0;
     measUFVolumeFromPriorReservoirs = 0.0;
-    // Send reset UF volumes to dialysate outlet pump
-    setDialOutUFVolumes( refUFVolume, measUFVolume );
+    setDialOutUFVolumes( refUFVolume, measUFVolume );  // Send reset UF volumes to dialysate outlet pump driver
 
     uFTimeMS = 0;
     lastUFTimeStamp = 0;
@@ -152,11 +154,12 @@
     uFAccuracyCheckTimerCtr = 0;
     lastUFVolumeChecked = 0.0;
 
-    for (i=0; i<NUM_OF_LOAD_CELLS; i++)
+    for ( i = 0; i<NUM_OF_LOAD_CELLS; i++ )
     {
         lcLastSteadyWeight[RESERVOIR_STEADY_CYCLE_START][i] = LOAD_CELL_ILLEGAL_WEIGHT_VALUE;
         lcLastSteadyWeight[RESERVOIR_STEADY_CYCLE_FINAL][i] = LOAD_CELL_ILLEGAL_WEIGHT_VALUE;
     }
+
     resetSalineBolus();
 }
 
@@ -215,32 +218,31 @@
     setValvePosition( VDO, VALVE_POSITION_B_OPEN );
     setValvePosition( VBA, VALVE_POSITION_B_OPEN );
     setValvePosition( VBV, VALVE_POSITION_B_OPEN );
-    // Restart pumps
 
+    // Restart pumps
 #ifndef _RELEASE_
     if ( SW_CONFIG_ENABLE_VALUE == getSoftwareConfigStatus( SW_CONFIG_ENABLE_BLOOD_PUMP_OPEN_LOOP ) )
     {
         mode = PUMP_CONTROL_MODE_OPEN_LOOP;
     }
 #endif
-
     setBloodPumpTargetFlowRate( setBloodFlowRate, MOTOR_DIR_FORWARD, mode );
-
 #ifndef _RELEASE_
     if ( SW_CONFIG_ENABLE_VALUE == getSoftwareConfigStatus( SW_CONFIG_ENABLE_DIALYSATE_INLET_PUMP_OPEN_LOOP ) )
     {
         mode = PUMP_CONTROL_MODE_OPEN_LOOP;
     }
 #endif
-
     setDialInPumpTargetFlowRate( setDialysateFlowRate, MOTOR_DIR_FORWARD, mode );
-
     setDialOutPumpTargetRate( setDialysateFlowRate + (S32)setUFRate, MOTOR_DIR_FORWARD, PUMP_CONTROL_MODE_CLOSED_LOOP );
+
     // Start Heparin pump as appropriate
     startHeparinPump();
+
     // Tell DG to start heating dialysate
     cmdStartDGTrimmerHeater();
 
+    // Start auto-control of air trap valve
     startAirTrapControl();
 
     // Set user alarm recovery actions allowed in this sub-mode
@@ -624,10 +626,6 @@
     // Dialysis state machine
     switch ( currentDialysisState )
     {
-        case DIALYSIS_START_STATE:
-            currentDialysisState = DIALYSIS_UF_STATE;
-            break;
-
         case DIALYSIS_UF_STATE:
             currentDialysisState = handleDialysisUltrafiltrationState();
             break;
@@ -641,6 +639,9 @@
             break;
     }
 
+    // Calculate UF measured volume and provide to dialysate outlet pump controller (watch UF regardless of dialysis state)
+    updateUFVolumes();
+
     // Publish saline bolus data at set interval (whether we are delivering one or not)
     publishSalineBolusData();
 }
@@ -669,10 +670,6 @@
     // Handle current ultrafiltration state
     switch ( currentUFState )
     {
-        case UF_START_STATE:
-            currentUFState = handleUFStartState( &result );
-            break;
-
         case UF_PAUSED_STATE:
             currentUFState = handleUFPausedState( &result );
             break;
@@ -731,24 +728,6 @@
 
 /*********************************************************************//**
  * @brief
- * The handleUFStartState function handles the Start state of the
- * ultrafiltration state machine.
- * @details Inputs: maxUFVolumeML
- * @details Outputs: if ultrafiltration prescribed, ultrafiltration time is
- * initialized.
- * @param dialysisState next dialysis state
- * @return next ultrafiltration state.
- *************************************************************************/
-static UF_STATE_T handleUFStartState( DIALYSIS_STATE_T *dialysisState )
-{
-    lastUFTimeStamp = getMSTimerCount();
-    uFTimeMS = 0;
-
-    return UF_RUNNING_STATE;
-}
-
-/*********************************************************************//**
- * @brief
  * The handleUFPausedState function handles the Paused state of the
  * ultrafiltration state machine.
  * @details Inputs: none
@@ -760,9 +739,6 @@
 {
     UF_STATE_T result = UF_PAUSED_STATE;
 
-    // Calculate UF volumes and provide to dialysate outlet pump controller
-    updateUFVolumes();
-
     // Handle saline bolus start request from user
     if ( TRUE == salineBolusStartRequested )
     {
@@ -810,9 +786,6 @@
         setUFRate = 0.0;
     }
 
-    // Calculate UF volumes and provide to dialysate outlet pump controller
-    updateUFVolumes();
-
     // Handle saline bolus start request from user
     if ( TRUE == salineBolusStartRequested )
     {
Index: firmware/App/Modes/ModeTreatment.c
===================================================================
diff -u -r0a4dcd288d4347b85baaa0b07da568b6add5eac7 -r33c3a81272ce8c9bae64ae20537e9be45b11edd0
--- firmware/App/Modes/ModeTreatment.c	(.../ModeTreatment.c)	(revision 0a4dcd288d4347b85baaa0b07da568b6add5eac7)
+++ firmware/App/Modes/ModeTreatment.c	(.../ModeTreatment.c)	(revision 33c3a81272ce8c9bae64ae20537e9be45b11edd0)
@@ -589,16 +589,19 @@
 {
     BOOL stop = isStopButtonPressed();
 
+    // Trigger user stop alarm at any time in treatment mode when user presses stop button
     if ( TRUE == stop )
     {
         activateAlarmNoData( ALARM_ID_TREATMENT_STOPPED_BY_USER );
     }
 
+    // Check dialysate temperature during treatment mode (except end state where treatment is over, dialyzer is bypassed and temp is no longer an issue)
     if ( currentTreatmentState != TREATMENT_END_STATE )
     {
         checkDialysateTemperature();
     }
 
+    // Record treatment start time if not done yet
     if ( FALSE == hasTreatmentStartTimeBeenWrittenToNV )
     {
         // Started the treatment set the start time in epoch