Index: firmware/App/Controllers/SyringePump.c
===================================================================
diff -u -r120487ddf3e3d69d1de5094d5252c037588e2ed8 -r53ded5e26646574d5bae2cebd5de47a2ac5a3c2d
--- firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision 120487ddf3e3d69d1de5094d5252c037588e2ed8)
+++ firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision 53ded5e26646574d5bae2cebd5de47a2ac5a3c2d)
@@ -1150,6 +1150,19 @@
 
 /*********************************************************************//**
  * @brief
+ * The isSyringePumpPositionKnown function returns whether the syringe
+ * pump position is known.
+ * @details \b Inputs: syringePumpPositionKnown
+ * @details \b Outputs: none
+ * @return TRUE if syringe pump position is known, otherwise FALSE.
+ *************************************************************************/
+BOOL isSyringePumpPositionKnown( void )
+{
+    return syringePumpPositionKnown;
+}
+
+/*********************************************************************//**
+ * @brief
  * The execSyringePumpMonitor function executes the syringe pump monitor.
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_RUNNING_WHILE_BP_OFF_ERROR
  * if syringe pump is running while the blood pump is off
Index: firmware/App/Controllers/SyringePump.h
===================================================================
diff -u -r120487ddf3e3d69d1de5094d5252c037588e2ed8 -r53ded5e26646574d5bae2cebd5de47a2ac5a3c2d
--- firmware/App/Controllers/SyringePump.h	(.../SyringePump.h)	(revision 120487ddf3e3d69d1de5094d5252c037588e2ed8)
+++ firmware/App/Controllers/SyringePump.h	(.../SyringePump.h)	(revision 53ded5e26646574d5bae2cebd5de47a2ac5a3c2d)
@@ -143,6 +143,7 @@
 BOOL isSyringePumpRunning( void );
 BOOL isSyringePumpPreLoaded( void );
 F32  getSyringePumpVolumeDelivered( void );
+BOOL isSyringePumpPositionKnown( void );
 
 BOOL testSyringePumpOperationRequest( MESSAGE_T *message );
 BOOL testSyringePumpDataPublishIntervalOverride( MESSAGE_T *message );
Index: firmware/App/Modes/ModePreTreat.c
===================================================================
diff -u -r9c96ad1bd9f61a3c6f979aebb1d9ccf1ec5529d7 -r53ded5e26646574d5bae2cebd5de47a2ac5a3c2d
--- firmware/App/Modes/ModePreTreat.c	(.../ModePreTreat.c)	(revision 9c96ad1bd9f61a3c6f979aebb1d9ccf1ec5529d7)
+++ firmware/App/Modes/ModePreTreat.c	(.../ModePreTreat.c)	(revision 53ded5e26646574d5bae2cebd5de47a2ac5a3c2d)
@@ -196,6 +196,10 @@
             // No action required.
             break;
 
+        case TD_PRE_TREATMENT_HEPARIN_SETUP_STATE:
+            // Heparin Setup transition is already handled in handleRxState().
+            break;
+
         case TD_PRE_TREATMENT_RECIRCULATE_STATE:
             // No action required.
             break;
Index: firmware/App/Modes/StatePreTxHeparinSetup.c
===================================================================
diff -u -r9c96ad1bd9f61a3c6f979aebb1d9ccf1ec5529d7 -r53ded5e26646574d5bae2cebd5de47a2ac5a3c2d
--- firmware/App/Modes/StatePreTxHeparinSetup.c	(.../StatePreTxHeparinSetup.c)	(revision 9c96ad1bd9f61a3c6f979aebb1d9ccf1ec5529d7)
+++ firmware/App/Modes/StatePreTxHeparinSetup.c	(.../StatePreTxHeparinSetup.c)	(revision 53ded5e26646574d5bae2cebd5de47a2ac5a3c2d)
@@ -50,6 +50,8 @@
 
 static BOOL heparinSetupResumeRequested;                                ///< Flag indicates alarm requesting to resume pre-treatment heparin setup.
 static BOOL syringeLoadConfirmed;                                       ///< Flag indicates user confirmed syringe load.
+static BOOL syringeRetractStarted;                                      ///< Flag indicating syringe retract has been initiated.
+static BOOL syringePreloadStarted;                                      ///< Flag indicating syringe preload has been initiated.
 
 // ********** private function prototypes **********
 
@@ -68,14 +70,19 @@
  * @brief
  * The initPreTxHeparinSetup function initializes the pre-treatment
  * heparin setup state machine.
- * @details Inputs: none
- * @details Outputs: Pre-treatment heparin setup initialized.
- * @return none
+ * @details \b Inputs: none.
+ * @details \b Outputs: currentPreTxHeparinSetupState,
+ * interruptedPreTxHeparinSetupState, syringeRetractStarted,
+ * syringePreloadStarted, heparinSetupResumeRequested, and
+ * syringeLoadConfirmed.
+ * @return none.
  *************************************************************************/
 void initPreTxHeparinSetup( void )
 {
     currentPreTxHeparinSetupState = PRE_TX_HEPARIN_SETUP_PRELOAD_STATE;
     interruptedPreTxHeparinSetupState = PRE_TX_HEPARIN_SETUP_PRELOAD_STATE;
+    syringeRetractStarted = FALSE;
+    syringePreloadStarted = FALSE;
 
     resetPreTxHeparinSetupFlags();
 }
@@ -84,22 +91,29 @@
  * @brief
  * The transitionToPreTxHeparinSetup function prepares for transition
  * into the pre-treatment heparin setup state.
- * @details Inputs: none
- * @details Outputs: Heparin setup initialized.
- * @return none
+ * @details \b Inputs: currentPreTxHeparinSetupState.
+ * @details \b Outputs: resume alarm user action enabled and current
+ * pre-treatment substate.
+ * @return none.
  *************************************************************************/
 void transitionToPreTxHeparinSetup( void )
 {
+    setAlarmUserActionEnabled( ALARM_USER_ACTION_RESUME, TRUE );
+
     setCurrentSubState( (U32)currentPreTxHeparinSetupState );
 }
 
 /*********************************************************************//**
  * @brief
  * The execPreTxHeparinSetup function executes the pre-treatment heparin
  * setup state machine.
- * @details Inputs: currentPreTxHeparinSetupState
- * @details Outputs: currentPreTxHeparinSetupState
- * @return none
+ * @details \b Alarm: ALARM_ID_TD_SOFTWARE_FAULT if the current
+ * pre-treatment heparin setup state is invalid.
+ * @details \b Inputs: currentPreTxHeparinSetupState.
+ * @details \b Outputs: currentPreTxHeparinSetupState, current substate,
+ * TD_EVENT_SUB_STATE_CHANGE event, heparinSetupResumeRequested, and
+ * syringeLoadConfirmed.
+ * @return none.
  *************************************************************************/
 void execPreTxHeparinSetup( void )
 {
@@ -154,8 +168,8 @@
  * @brief
  * The getPreTxHeparinSetupState function returns the current state of the
  * pre-treatment heparin setup state machine.
- * @details Inputs: currentPreTxHeparinSetupState
- * @details Outputs: none
+ * @details \b Inputs: currentPreTxHeparinSetupState.
+ * @details \b Outputs: none.
  * @return Current pre-treatment heparin setup state.
  *************************************************************************/
 U32 getPreTxHeparinSetupState( void )
@@ -167,9 +181,9 @@
  * @brief
  * The signalResumePreTxHeparinSetup function signals a resume request for
  * the pre-treatment heparin setup state machine.
- * @details Inputs: none
- * @details Outputs: heparinSetupResumeRequested
- * @return none
+ * @details \b Inputs: none.
+ * @details \b Outputs: heparinSetupResumeRequested.
+ * @return none.
  *************************************************************************/
 void signalResumePreTxHeparinSetup( void )
 {
@@ -194,9 +208,9 @@
  * @brief
  * The signalPreTxHeparinSyringeLoadConfirmed function signals that the
  * user confirmed syringe load.
- * @details Inputs: none
- * @details Outputs: syringeLoadConfirmed
- * @return none
+ * @details \b Inputs: none.
+ * @details \b Outputs: syringeLoadConfirmed.
+ * @return none.
  *************************************************************************/
 void signalPreTxHeparinSyringeLoadConfirmed( void )
 {
@@ -207,9 +221,10 @@
  * @brief
  * The resetPreTxHeparinSetupFlags function resets all signal flags used by
  * the pre-treatment heparin setup state machine.
- * @details Inputs: none
- * @details Outputs: Signal flags reset.
- * @return none
+ * @details \b Inputs: none.
+ * @details \b Outputs: heparinSetupResumeRequested and
+ * syringeLoadConfirmed.
+ * @return none.
  *************************************************************************/
 static void resetPreTxHeparinSetupFlags( void )
 {
@@ -221,9 +236,10 @@
  * @brief
  * The setupPreTxHeparinState function configures the syringe pump for the
  * specified pre-treatment heparin setup state.
- * @details Inputs: state
- * @details Outputs: Syringe pump configured for the specified state.
- * @return none
+ * @details \b Inputs: none.
+ * @details \b Outputs: syringe pump operating state.
+ * @param state Pre-treatment heparin setup state to configure.
+ * @return none.
  *************************************************************************/
 static void setupPreTxHeparinState( PRE_TX_HEPARIN_SETUP_STATE_T state )
 {
@@ -232,9 +248,9 @@
     switch ( state )
     {
         case PRE_TX_HEPARIN_SETUP_PRELOAD_STATE:
-            resetPreLoadStatus();
-            preloadSyringePlunger();
-            break;
+        // Retract and preload sequencing is handled by
+        // handlePreTxHeparinPreloadState().
+         break;
 
         case PRE_TX_HEPARIN_SETUP_SEEK_STATE:
             seekSyringePlunger();
@@ -263,9 +279,16 @@
 
 /*********************************************************************//**
  * @brief
- * The handlePreTxHeparinPreloadState function handles the preload state.
- * @details \b Inputs: none
- * @details \b Outputs: Next pre-treatment heparin setup state.
+ * The handlePreTxHeparinPreloadState function handles the syringe pump
+ * retract and preload sequence.
+ * @details \b Alarm: ALARM_ID_UI_RESERVED_127 when syringe preload is
+ * complete and syringe loading confirmation is required.
+ * @details \b Inputs: syringeRetractStarted, syringePreloadStarted,
+ * alarm stop status, syringe pump position, preload status, and syringe
+ * pump operating status.
+ * @details \b Outputs: interruptedPreTxHeparinSetupState,
+ * syringeRetractStarted, syringePreloadStarted, syringe pump operating
+ * state, and preload status.
  * @return Current or next pre-treatment heparin setup state.
  *************************************************************************/
 static PRE_TX_HEPARIN_SETUP_STATE_T handlePreTxHeparinPreloadState( void )
@@ -278,25 +301,38 @@
         setupPreTxHeparinState( PRE_TX_HEPARIN_SETUP_PAUSED_STATE );
         state = PRE_TX_HEPARIN_SETUP_PAUSED_STATE;
     }
-    else if ( ( FALSE == isSyringePumpRunning() ) && ( FALSE == isSyringePumpPreLoaded() ) )
-    {
-        setupPreTxHeparinState( PRE_TX_HEPARIN_SETUP_PRELOAD_STATE );
-    }
     else if ( TRUE == isSyringePumpPreLoaded() )
     {
         activateAlarmNoData( ALARM_ID_UI_RESERVED_127 );
         state = PRE_TX_HEPARIN_SETUP_AWAIT_SYRINGE_LOAD_CONFIRMATION_STATE;
     }
+    else if ( FALSE == isSyringePumpPositionKnown() )
+    {
+        if ( ( FALSE == syringeRetractStarted ) &&  ( FALSE == isSyringePumpRunning() ) )
+        {
+            syringeRetractStarted = retractSyringePump();
+        }
+    }
+    else if ( FALSE == syringePreloadStarted )
+    {
+        if ( FALSE == isSyringePumpRunning() )
+        {
+            resetPreLoadStatus();
 
+            syringePreloadStarted = preloadSyringePlunger();
+        }
+    }
+
     return state;
 }
 
 /*********************************************************************//**
  * @brief
  * The handlePreTxHeparinAwaitSyringeLoadConfirmationState function handles
  * the await syringe load confirmation state.
- * @details \b Inputs: none
- * @details \b Outputs: Next pre-treatment heparin setup state.
+ * @details \b Inputs: syringeLoadConfirmed and alarm stop status.
+  * @details \b Outputs: interruptedPreTxHeparinSetupState and syringe
+ * pump operating state.
  * @return Current or next pre-treatment heparin setup state.
  *************************************************************************/
 static PRE_TX_HEPARIN_SETUP_STATE_T handlePreTxHeparinAwaitSyringeLoadConfirmationState( void )
@@ -320,11 +356,12 @@
 
 /*********************************************************************//**
  * @brief
- * The handlePreTxHeparinSeekState function handles the seek state.
- * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_NOT_ENOUGH_HEPARIN_ALARM
- * if the syringe contains insufficient heparin for the prescribed treatment.
- * @details \b Inputs: none
- * @details \b Outputs: Next pre-treatment heparin setup state.
+ * The handlePreTxHeparinSeekState function handles the syringe plunger
+ * seek state.
+ * @details \b Inputs: alarm stop status, syringe plunger status, and
+ * syringe volume adequacy status.
+ * @details \b Outputs: interruptedPreTxHeparinSetupState and syringe
+ * pump operating state.
  * @return Current or next pre-treatment heparin setup state.
  *************************************************************************/
 static PRE_TX_HEPARIN_SETUP_STATE_T handlePreTxHeparinSeekState( void )
@@ -357,9 +394,11 @@
 
 /*********************************************************************//**
  * @brief
- * The handlePreTxHeparinPrimeState function handles the prime state.
- * @details \b Inputs: none
- * @details \b Outputs: Next pre-treatment heparin setup state.
+ * The handlePreTxHeparinPrimeState function handles the syringe pump
+ * prime state.
+ * @details \b Inputs: alarm stop status and syringe pump prime status.
+ * @details \b Outputs: interruptedPreTxHeparinSetupState and syringe
+ * pump operating state.
  * @return Current or next pre-treatment heparin setup state.
  *************************************************************************/
 static PRE_TX_HEPARIN_SETUP_STATE_T handlePreTxHeparinPrimeState( void )
@@ -385,10 +424,12 @@
  * @brief
  * The handlePreTxHeparinOcclusionCheckState function handles the heparin
  * pump occlusion check state.
- * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_OCCLUSION if the
- * heparin pump occlusion check fails.
- * @details \b Inputs: none
- * @details \b Outputs: Next pre-treatment heparin setup state.
+ * @details \b Alarm: ALARM_ID_TD_SYRINGE_PUMP_OCCLUSION if the syringe
+ * pump occlusion check fails.
+ * @details \b Inputs: alarm stop status, syringe pump occlusion status,
+ * and TREATMENT_PARAM_HEPARIN_BOLUS_VOLUME.
+ * @details \b Outputs: interruptedPreTxHeparinSetupState, syringe pump
+ * operating state, and pre-treatment continuation request.
  * @return Current or next pre-treatment heparin setup state.
  *************************************************************************/
 static PRE_TX_HEPARIN_SETUP_STATE_T handlePreTxHeparinOcclusionCheckState( void )
@@ -427,9 +468,11 @@
 
 /*********************************************************************//**
  * @brief
- * The handlePreTxHeparinBolusState function handles the bolus state.
- * @details \b Inputs: none
- * @details \b Outputs: Next pre-treatment heparin setup state.
+ * The handlePreTxHeparinBolusState function handles the heparin bolus
+ * state.
+ * @details \b Inputs: alarm stop status and syringe pump stop status.
+ * @details \b Outputs: interruptedPreTxHeparinSetupState, syringe pump
+ * operating state, and pre-treatment continuation request.
  * @return Current or next pre-treatment heparin setup state.
  *************************************************************************/
 static PRE_TX_HEPARIN_SETUP_STATE_T handlePreTxHeparinBolusState( void )
@@ -452,11 +495,14 @@
 
 /*********************************************************************//**
  * @brief
- * The handlePreTxHeparinPausedState function handles the paused state.
- * @details \b Inputs: heparinSetupResumeRequested,
- * interruptedPreTxHeparinSetupState
- * @details \b Outputs: Next pre-treatment heparin setup state and
- * syringe pump operation.
+ * The handlePreTxHeparinPausedState function handles the paused
+ * pre-treatment heparin setup state.
+ * @details \b Alarm: ALARM_ID_TD_SOFTWARE_FAULT if the interrupted
+ * pre-treatment heparin setup state is invalid.
+ * @details \b Inputs: heparinSetupResumeRequested and
+ * interruptedPreTxHeparinSetupState.
+ * @details \b Outputs: syringeRetractStarted, syringePreloadStarted,
+ * preload status, and syringe pump operating state.
  * @return Current or next pre-treatment heparin setup state.
  *************************************************************************/
 static PRE_TX_HEPARIN_SETUP_STATE_T handlePreTxHeparinPausedState( void )
@@ -472,7 +518,11 @@
             case PRE_TX_HEPARIN_SETUP_PRELOAD_STATE:
             case PRE_TX_HEPARIN_SETUP_AWAIT_SYRINGE_LOAD_CONFIRMATION_STATE:
             case PRE_TX_HEPARIN_SETUP_SEEK_STATE:
-                retractSyringePump();
+                syringeRetractStarted = FALSE;
+                syringePreloadStarted = FALSE;
+                resetPreLoadStatus();
+                syringeRetractStarted = retractSyringePump();
+
                 state = PRE_TX_HEPARIN_SETUP_PRELOAD_STATE;
                 break;