diff --git a/NanoJ-Fluidics.jar b/NanoJ-Fluidics.jar
index 491ed37..e6a8665 100644
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diff --git a/NanoJ-Fluidics_IJ.jar b/NanoJ-Fluidics_IJ.jar
index 3d6abfc..de6cd4b 100644
Binary files a/NanoJ-Fluidics_IJ.jar and b/NanoJ-Fluidics_IJ.jar differ
diff --git a/NanoJ-Fluidics_MM.jar b/NanoJ-Fluidics_MM.jar
index 7a25d58..b2f3b76 100644
Binary files a/NanoJ-Fluidics_MM.jar and b/NanoJ-Fluidics_MM.jar differ
diff --git a/PackagedBinaries/NanoJ-Fluidics.zip b/PackagedBinaries/NanoJ-Fluidics.zip
index 0740f78..589d282 100644
Binary files a/PackagedBinaries/NanoJ-Fluidics.zip and b/PackagedBinaries/NanoJ-Fluidics.zip differ
diff --git a/PackagedBinaries/NanoJ-Fluidics_IJ.zip b/PackagedBinaries/NanoJ-Fluidics_IJ.zip
index edc8b51..30817d3 100644
Binary files a/PackagedBinaries/NanoJ-Fluidics_IJ.zip and b/PackagedBinaries/NanoJ-Fluidics_IJ.zip differ
diff --git a/PackagedBinaries/NanoJ-Fluidics_MM.zip b/PackagedBinaries/NanoJ-Fluidics_MM.zip
index 6140970..faf2a1a 100644
Binary files a/PackagedBinaries/NanoJ-Fluidics_MM.zip and b/PackagedBinaries/NanoJ-Fluidics_MM.zip differ
diff --git a/src/nanoj/pumpControl/java/sequentialProtocol/SequenceManager.java b/src/nanoj/pumpControl/java/sequentialProtocol/SequenceManager.java
index 19e3630..8be9af1 100644
--- a/src/nanoj/pumpControl/java/sequentialProtocol/SequenceManager.java
+++ b/src/nanoj/pumpControl/java/sequentialProtocol/SequenceManager.java
@@ -40,7 +40,7 @@ private SequenceManager() { }
     public void run(){
         while (alive) {
             if (started) {
-                for (currentStep = startStep; currentStep < endStep+1; currentStep++) {
+                for (currentStep = startStep; currentStep < endStep; currentStep++) {
                     if (!started) break;
 
                     Step step = sequence.get(currentStep);
@@ -105,14 +105,16 @@ else if (timeToGo >= 60) setWaitingMessage("Withdrawal step. Waiting for: "
 
                     // If this isn't the last step, then set the "syringe ready" status to false. This makes
                     // the sequence wait until the user has confirmed the syringe exchange.
-                    if (currentStep != endStep) setMonkeyReady(false);
+                    if (currentStep < endStep) setMonkeyReady(false);
                         // If it IS the last step, then we can stop now.
                     else {
                         stop();
+                        setWaitingMessage("Sequence finished.");
                         break;
                     }
 
-                    syringeExchangeNeeded = sequence.get(currentStep+1).isSyringeExchangeRequired();
+                    if (currentStep < endStep-1)
+                        syringeExchangeNeeded = sequence.get(currentStep+1).isSyringeExchangeRequired();
 
                     setChanged();
                     notifyObservers(SYRINGE_STATUS_CHANGED);
@@ -146,6 +148,8 @@ else if (timeToGo >= 60) setWaitingMessage("Step: " + step.getNumber() + ", "
                     }
                 }
                 currentStep = -1;
+                endStep = 0;
+                started = false;
                 setChanged();
                 notifyObservers(SEQUENCE_FINISHED);
             }