Index: firmware/App/Controllers/SyringePump.c
===================================================================
diff -u -rd3b7ae356aae29c99cb039713a2e120fdbce5a9c -rd951c4a673f308306d48650182c3af3814e9ab4b
--- firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision d3b7ae356aae29c99cb039713a2e120fdbce5a9c)
+++ firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision d951c4a673f308306d48650182c3af3814e9ab4b)
@@ -429,7 +429,12 @@
  *************************************************************************/
 BOOL retractSyringePump( void )
 {
+#ifndef ALWAYS_ALLOW_SYRINGE_PUMP_CMDS
     if ( ( SYRINGE_PUMP_OFF_STATE == syringePumpState ) && ( heparinDeliveryState != HEPARIN_STATE_OFF ) )
+#else
+    heparinDeliveryState = HEPARIN_STATE_STOPPED;
+    if ( ( SYRINGE_PUMP_OFF_STATE == syringePumpState ) )
+#endif
     {
         syringePumpSetRate = SYRINGE_PUMP_RETRACT_RATE;
         syringePumpRetractRequested = TRUE;
@@ -825,11 +830,13 @@
 
     if ( syringePumpDACVrefWriteInProgress != TRUE )
     {
-        // Check ADC read is fresh
-        if ( lastSyringePumpADCReadCtr == adcReadCtr )  // TODO - add persistence
+#ifndef USING_DEBUGGER
+        // Check ADC read is fresh (takes FPGA a while to configure ADC so don't check until after init/POST mode
+        if ( ( getCurrentOperationMode() > MODE_INIT ) && ( lastSyringePumpADCReadCtr == adcReadCtr ) ) // TODO - add persistence or time window
         {
-            // activateAlarmNoData( ALARM_ID_HD_SYRINGE_PUMP_ADC_ERROR );  // TODO - restore when issue with read counter resolved
+            activateAlarmNoData( ALARM_ID_HD_SYRINGE_PUMP_ADC_ERROR );
         }
+#endif
         lastSyringePumpADCReadCtr = adcReadCtr;
 
         //  Check encoder direction error.  // TODO check direction in states