Index: firmware/App/Controllers/SyringePump.c
===================================================================
diff -u -r3250a641e46b5338671a5b830189ffb3694d1284 -r8d1ae378f26055b881c2b06b7163997d858b1342
--- firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision 3250a641e46b5338671a5b830189ffb3694d1284)
+++ firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision 8d1ae378f26055b881c2b06b7163997d858b1342)
@@ -65,7 +65,7 @@
 #ifndef SLOW_SYRINGE_RETRACT
 #define SYRINGE_PUMP_RETRACT_RATE                     10800.0                               ///< Retract rate is 15 mL/ 5 s = 3 mL/s = 10,800 mL/hr.
 #else
-#define SYRINGE_PUMP_RETRACT_RATE                     3600.0                                ///< Retract rate is 15 mL/ 5 s = 3 mL/s = 10,800 mL/hr.
+#define SYRINGE_PUMP_RETRACT_RATE                     3600.0                                ///< Retract rate is 5 mL/ 5 s = 1 mL/s = 3,600 mL/hr.
 #endif
 #define SYRINGE_PUMP_SEEK_RATE                        3600.0                                ///< Seek plunger rate is 5 mL/ 5 s = 1 mL/s = 3,600 mL/hr.
 #define SYRINGE_PUMP_PRIME_RATE                       635.0                                 ///< Prime rate is 0.5 mm ^ 2 x PI x 450 mm = 0.353 mL / 2s = 635 mL/hr.
@@ -249,6 +249,7 @@
 static BOOL checkMaxTravel( BOOL stopPump, S32 maxPos );
 static BOOL checkMeasRate( BOOL stopPump, F32 pctMargin );
 static BOOL checkVolumeVsSafetyVolume( BOOL stopPump, F32 pctMargin );
+static BOOL checkForStall( BOOL stopPump );
 static void publishSyringePumpData( void );
 
 /*********************************************************************//**
@@ -1142,6 +1143,9 @@
         // Calculate target FPGA rate from set rate in mL/hr converted to microstep toggle interval in uSec
         calcStepperToggleTimeForTargetRate( syringePumpSetRate );
         setFPGASyringePumpStepToggleTime( syringePumpRampUpToggleTime );
+        // Reset stall detect variables
+        syringePumpStallRetryCount = 0;
+        syringePumpStallCtr = 0;
     }
 
     // Reset ramp up timer
@@ -1163,31 +1167,7 @@
     SYRINGE_PUMP_STATE_T result = SYRINGE_PUMP_RETRACT_STATE;
     BOOL stopPump = FALSE;
 
-    // Check for stall
-    if ( fabs( getSyringePumpMeasRate() ) < SYRINGE_PUMP_STALL_SPEED_THRESHOLD )
-    {
-        if ( ++syringePumpStallCtr > SYRINGE_PUMP_RAMP_STALL_TIME )
-        {
-            if ( ++syringePumpStallRetryCount <= SYRINGE_PUMP_RAMP_STALL_RETRIES )
-            {
-                syringePumpSetToggleTime++;   // lower target rate
-                syringePumpRampTimerCtr = 0;  // restart ramp
-                syringePumpRampUpToggleTime = SYRINGE_PUMP_START_RAMP_SPEED;
-                syringePumpStallCtr = 0;      // reset stall counter
-            }
-            else
-            {
-                stopPump = TRUE;
-                // TODO - stall alarm?
-            }
-        }
-    }
-    else
-    {
-        syringePumpStallCtr = 0;
-    }
-
-    // Handle ramp up
+     // Handle ramp up
     rampSyringePump();
 
     // Stop retract when home position is detected
@@ -1216,6 +1196,8 @@
         SET_ALARM_WITH_2_U32_DATA( ALARM_ID_HD_SYRINGE_PUMP_OVER_TRAVEL_ERROR, (U32)getSyringePumpPosition(), (U32)SYRINGE_PUMP_RETRACT_STATE );
     }
 
+    stopPump = checkForStall( stopPump );
+
     stopPump = checkDirection( stopPump, MOTOR_DIR_REVERSE );
 
     // If anything found that would require stopping the pump, stop pump and go to off state
@@ -1648,6 +1630,33 @@
     return result;
 }
 
+static BOOL checkForStall( BOOL stopPump )
+{
+    // Check for stall
+     if ( fabs( getSyringePumpMeasRate() ) < SYRINGE_PUMP_STALL_SPEED_THRESHOLD )
+     {
+         if ( ++syringePumpStallCtr > SYRINGE_PUMP_RAMP_STALL_TIME )
+         {
+             if ( ++syringePumpStallRetryCount <= SYRINGE_PUMP_RAMP_STALL_RETRIES )
+             {
+                 syringePumpSetToggleTime++;   // lower target rate
+                 syringePumpRampTimerCtr = 0;  // restart ramp
+                 syringePumpRampUpToggleTime = SYRINGE_PUMP_START_RAMP_SPEED;
+                 syringePumpStallCtr = 0;      // reset stall counter
+             }
+             else
+             {
+                 stopPump = TRUE;
+                 SET_ALARM_WITH_2_U32_DATA( ALARM_ID_HD_SYRINGE_PUMP_STALL, (U32)getSyringePumpPosition(), (U32)syringePumpState );
+             }
+         }
+     }
+     else
+     {
+         syringePumpStallCtr = 0;
+     }
+}
+
 /*********************************************************************//**
  * @brief
  * The rampSyringePump function handles the ramp-up for the syringe pump.