diff --git a/uk/ac/sanger/artemis/components/GraphMenu.java b/uk/ac/sanger/artemis/components/GraphMenu.java
index 449c3afb580d9376c04f5eb889a6f361d3c74e3a..72b05f3cd27a8fcd01a769e0652b103ffa1e4f40 100644
--- a/uk/ac/sanger/artemis/components/GraphMenu.java
+++ b/uk/ac/sanger/artemis/components/GraphMenu.java
@@ -107,7 +107,8 @@ public class GraphMenu extends JMenu
                     final BasePlotGroup base_plot_group,
                     final FeatureDisplay feature_display,
                     final String menu_name, 
-                    final JSplitPane splitPane) 
+                    final JSplitPane splitPane,
+                    final int index) 
   {
     super (menu_name);
     this.frame = frame;
@@ -244,9 +245,9 @@ public class GraphMenu extends JMenu
     }
     
     // add user plots from the command line JVM option
-    if(System.getProperty("userplot") != null)
+    if(System.getProperty("userplot"+ (index > 0 ? index : "")) != null)
     {
-      String plots[] = System.getProperty("userplot").split("[\\s,]");
+      String plots[] = System.getProperty("userplot"+ (index > 0 ? index : "")).split("[\\s,]");
       try
       {
         for(int i=0;i<plots.length; i++)
@@ -294,7 +295,7 @@ public class GraphMenu extends JMenu
                     final FeatureDisplay feature_display,
                     final JSplitPane splitPane) 
   {
-    this (frame, entry_group, base_plot_group, feature_display, "Graph",splitPane);
+    this (frame, entry_group, base_plot_group, feature_display, "Graph",splitPane, -1);
   }
 
   /**
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index f8528bd9319797b5cd12e6e9bfb9176eb5edf3f3..751605414e3f96373794bc47dd72670f43d8d195 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.java
@@ -711,13 +711,6 @@ public class MultiComparator extends JFrame
                       sub_menu_name);
         create_menu.add(this_create_menu);
 
-        /*final WriteMenu this_write_menu =
-          new WriteMenu(this,
-                         getSelectionArray()[i],
-                         getEntryGroupArray()[i],
-                         sub_menu_name);
-        write_menu.add(this_write_menu);*/
-
         if(Options.isUnixHost()) 
         {
           final RunMenu this_run_menu =
@@ -733,7 +726,7 @@ public class MultiComparator extends JFrame
                        getEntryGroupArray()[i],
                        getBasePlotGroupArray()[i],
                        getFeatureDisplayArray()[i],
-                       sub_menu_name, null);
+                       sub_menu_name, null, i+1);
       graph_menu.add(this_graph_menu);
     }