diff --git a/config/scripts/duty.sc b/config/scripts/duty.sc
index 648380f068..6d6b205261 100644
--- a/config/scripts/duty.sc
+++ b/config/scripts/duty.sc
@@ -1,7 +1,7 @@
 echo "#!type line" | window duty
-duty 10 "MSP430 Core.active" CC2420.listen CC2420.transmit "Tmote Sky.0" | window duty
 echo "#!set 0 label CPU" | window duty
 echo "#!set 1 label Listen" | window duty
 echo "#!set 2 label Transmit" | window duty
 echo "#!set 3 label LEDS" | window duty
-echo "#!title Duty Cycle" | window duty
\ No newline at end of file
+echo "#!title Duty Cycle" | window duty
+duty 10 "MSP430 Core.active" CC2420.listen CC2420.transmit "Tmote Sky.0" | window duty
diff --git a/java/se/sics/mspsim/cli/Command.java b/java/se/sics/mspsim/cli/Command.java
index c40870dc54..24ab2ca020 100644
--- a/java/se/sics/mspsim/cli/Command.java
+++ b/java/se/sics/mspsim/cli/Command.java
@@ -23,7 +23,7 @@ public abstract class Command {
   public abstract int executeCommand(CommandContext context);
 
   /* default behavior is that it returns *this* instance (which might be bad in some cases) */
-  public Object getInstance() {
+  public Command getInstance() {
       return this;
   }
 }
diff --git a/java/se/sics/mspsim/cli/CommandHandler.java b/java/se/sics/mspsim/cli/CommandHandler.java
index e45b5b40e4..d58e2e3276 100644
--- a/java/se/sics/mspsim/cli/CommandHandler.java
+++ b/java/se/sics/mspsim/cli/CommandHandler.java
@@ -1,6 +1,7 @@
 package se.sics.mspsim.cli;
 import java.io.File;
 import java.io.PrintStream;
+import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -128,15 +129,45 @@ public int executeCommand(String commandLine, CommandContext context) {
     return -1;
   }
 
+  private File resolveScript(String script) {
+    // Only search for script files
+    if (!script.endsWith(".sc")) {
+      return null;
+    }
+    var scriptFile = new File(scriptDirectory, script);
+    if (scriptFile.exists()) {
+      return scriptFile;
+    }
+    scriptFile = new File("config/scripts", script);
+    if (scriptFile.exists()) {
+      return scriptFile;
+    }
+    File parent;
+    try {
+      parent = new File(CommandHandler.class.getProtectionDomain().getCodeSource().getLocation().toURI())
+              .getParentFile().getParentFile();
+    } catch (URISyntaxException e) {
+      parent = null;
+    }
+    if (parent != null) {
+      var scriptPath = "resources/main/scripts/" + script;
+      scriptFile = new File(parent, scriptPath);
+      if (!scriptFile.exists()) { // Running from gradle
+        scriptFile= new File(parent.getParentFile(), scriptPath);
+      }
+    }
+    return scriptFile.exists() ? scriptFile : null;
+  }
+
   // This will return an instance that can be configured -
   // which is basically not OK... TODO - fix this!!!
   private Command getCommand(String cmd)  {
     Command command = commands.get(cmd);
     if (command != null) {
-        return (Command) command.getInstance();
+        return command.getInstance();
     }
-    File scriptFile = new File(scriptDirectory, cmd);
-    if (scriptFile.isFile() && scriptFile.canRead()) {
+    File scriptFile = resolveScript(cmd);
+    if (scriptFile != null && scriptFile.isFile() && scriptFile.canRead()) {
       return new ScriptCommand(scriptFile);
     }
     return null;
diff --git a/java/se/sics/mspsim/cli/WindowTarget.java b/java/se/sics/mspsim/cli/WindowTarget.java
index 9764dde5c4..b67155c2a6 100644
--- a/java/se/sics/mspsim/cli/WindowTarget.java
+++ b/java/se/sics/mspsim/cli/WindowTarget.java
@@ -41,6 +41,9 @@ private void processLine(CommandContext context, String line) {
     if (line.startsWith("#!")) {
       line = line.substring(2);
       String[] parts = CommandParser.parseLine(line);
+      if (parts == null || parts.length == 0) {
+        return;
+      }
       String cmd = parts[0];
       if ("bounds".equals(cmd)) {
         try {
@@ -56,6 +59,7 @@ private void processLine(CommandContext context, String line) {
           dataHandler.setProperty("title", new String[] {args});
         }
       } else if ("type".equals(cmd)) {
+        var hasOldDataHandler = dataHandler != null;
         if ("line-sample".equals(parts[1])) {
           dataHandler = new LineSampleChart();
         } else if ("line".equals(parts[1])) {
@@ -64,9 +68,11 @@ private void processLine(CommandContext context, String line) {
           context.err.println("Unknown window data handler type: " + parts[1]);
         }
         if (dataHandler != null) {
-          System.out.println("Replacing window data handler! " + parts[1] + " " + dataHandler);
+          if (hasOldDataHandler) {
+            System.out.println("Replacing window data handler! " + parts[1] + " " + dataHandler);
+            window.removeAll();
+          }
           JComponent dataComponent = dataHandler.getComponent();
-          window.removeAll();
           window.add(dataComponent);
           String title = window.getTitle();
           if (title != null) {
diff --git a/java/se/sics/mspsim/extutil/jfreechart/JFreeWindowDataHandler.java b/java/se/sics/mspsim/extutil/jfreechart/JFreeWindowDataHandler.java
index ce987065fa..3b62e0578a 100644
--- a/java/se/sics/mspsim/extutil/jfreechart/JFreeWindowDataHandler.java
+++ b/java/se/sics/mspsim/extutil/jfreechart/JFreeWindowDataHandler.java
@@ -40,6 +40,8 @@
  */
 package se.sics.mspsim.extutil.jfreechart;
 
+import java.util.ArrayList;
+import java.util.HashMap;
 import org.jfree.data.general.Series;
 import se.sics.mspsim.cli.AbstractWindowDataHandler;
 
@@ -49,6 +51,16 @@
  */
 public abstract class JFreeWindowDataHandler extends AbstractWindowDataHandler {
 
+  private HashMap<Integer,String> labelMap = new HashMap<>();
+
+  protected String getDataSeriesLabel(int index) {
+    return labelMap.get(index);
+  }
+
+  protected String getDataSeriesLabel(int index, String defaultLabel) {
+    var label = getDataSeriesLabel(index);
+    return label != null ? label : defaultLabel;
+  }
 
   public abstract int getDataSeriesCount();
   public abstract Series getDataSeries(int index);
@@ -58,13 +70,8 @@ public abstract class JFreeWindowDataHandler extends AbstractWindowDataHandler {
    */
   @Override
   public void setProperty(int index, String param, String[] args) {
-    if (index > getDataSeriesCount()) {
-      throw new IndexOutOfBoundsException("Illegal index: " + index);
-    }
     if ("label".equals(param)) {
-      getDataSeries(index).setKey(args[0]);
-      getComponent().revalidate();
-      getComponent().repaint();
+      labelMap.put(index, args[0]);
     }
   }
 
diff --git a/java/se/sics/mspsim/extutil/jfreechart/LineChart.java b/java/se/sics/mspsim/extutil/jfreechart/LineChart.java
index 64708b31d9..d5d414efdb 100644
--- a/java/se/sics/mspsim/extutil/jfreechart/LineChart.java
+++ b/java/se/sics/mspsim/extutil/jfreechart/LineChart.java
@@ -114,10 +114,11 @@ public void setProperty(String param, String[] args) {
   }
 
   private void addSeries() {
-    XYSeries dataSeries = new XYSeries("series " + (getDataSeriesCount() + 1));
+    int index = getDataSeriesCount();
+    XYSeries dataSeries = new XYSeries(getDataSeriesLabel(index, "series " + (index + 1)));
     dataSeries.setMaximumItemCount(200);
 //    renderer.setSeriesPaint(0, Color.black);
-    renderer.setSeriesShapesVisible(getDataSeriesCount(), false);
+    renderer.setSeriesShapesVisible(index, false);
     dataset.addSeries(dataSeries);
   }
 
diff --git a/java/se/sics/mspsim/ui/JFrameWindowManager.java b/java/se/sics/mspsim/ui/JFrameWindowManager.java
index 20668ff4f3..a91a8b6412 100644
--- a/java/se/sics/mspsim/ui/JFrameWindowManager.java
+++ b/java/se/sics/mspsim/ui/JFrameWindowManager.java
@@ -28,16 +28,17 @@ public void pack() {
 
             @Override
             public void add(Component component) {
-                window.add(component);
+                window.getContentPane().add(component);
                 if (!restored) {
                     restored = true;
                     WindowUtils.restoreWindowBounds(name, window);
                 }
+                window.revalidate();
             }
 
             @Override
             public void removeAll() {
-                window.removeAll();
+                window.getContentPane().removeAll();
             }
 
             @Override