diff --git a/uk/ac/sanger/artemis/components/NonModalDialog.java b/uk/ac/sanger/artemis/components/NonModalDialog.java
new file mode 100644
index 0000000000000000000000000000000000000000..bb344953c17c97cedc448683a74186983ef94405
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/NonModalDialog.java
@@ -0,0 +1,95 @@
+/* NonModalDialog
+ *
+ * created: 2011
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2011  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.components;
+
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.FontMetrics;
+import java.awt.GraphicsConfiguration;
+import java.awt.GraphicsDevice;
+import java.awt.GraphicsEnvironment;
+import java.awt.Insets;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+
+public class NonModalDialog extends JDialog
+{
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Create a non-modal dialog with an array of strings to
+   * display on separate lines.
+   * @param f
+   * @param labelStr
+   */
+  public NonModalDialog(JFrame f, String labelStr[])
+  {
+    super(f, "Check the reference is correctly selected", false);
+    
+    GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
+    GraphicsDevice gd = ge.getDefaultScreenDevice();
+    GraphicsConfiguration gc = gd.getDefaultConfiguration();
+    Insets ins = Toolkit.getDefaultToolkit().getScreenInsets(gc);
+    int sw = gc.getBounds().width - ins.left - ins.right;
+    int sh = gc.getBounds().height - ins.top - ins.bottom;
+
+    setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+    Container cp = getContentPane();
+    Box yBox = Box.createVerticalBox();
+    cp.setLayout(new BorderLayout());
+        
+    int width = 10;
+    for(int i=0; i<labelStr.length; i++)
+    {
+      JLabel label = new JLabel(labelStr[i]);
+      yBox.add(label);
+      
+      FontMetrics fm = label.getFontMetrics(label.getFont());
+      int thisWidth = fm.stringWidth(label.getText());
+      if(thisWidth > width)
+        width = thisWidth;
+    }
+    cp.add(yBox, BorderLayout.NORTH);
+    
+    JButton okButton = new JButton("OK");
+    cp.add(okButton, BorderLayout.SOUTH);
+    okButton.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent arg0)
+      {
+        dispose();
+      }
+    });
+
+    setBounds((sw - width)/2, sh/2, width, 100);
+    setVisible(true);
+  }
+}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 50c427cd5c32b97559f735d115d728543d8b5567..a5749e6e2c82e79d5c3e72c2f77582fe331d73cd 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -116,6 +116,7 @@ import uk.ac.sanger.artemis.components.EntryFileDialog;
 import uk.ac.sanger.artemis.components.FeatureDisplay;
 import uk.ac.sanger.artemis.components.FileViewer;
 import uk.ac.sanger.artemis.components.MessageDialog;
+import uk.ac.sanger.artemis.components.NonModalDialog;
 import uk.ac.sanger.artemis.components.SwingWorker;
 import uk.ac.sanger.artemis.components.genebuilder.AutoCompleteComboDocument;
 import uk.ac.sanger.artemis.components.variant.FeatureContigPredicate;
@@ -1980,13 +1981,16 @@ public class BamView extends JPanel
             }
           }
 
-          JOptionPane.showMessageDialog(null, 
-              "The length of the sequence loaded does not match the length of\n"+
-              "the default reference sequence in the BAM ("+seqNames.get(0)+").\n"+
-              (newIndex == -1 ? "" : "The length does match the reference "+
-                  seqNames.get(newIndex)+" so this has been\nset as the default."), 
-                  "Check the reference is correctly selected", 
-                  JOptionPane.WARNING_MESSAGE);
+          if(!Options.isBlackBeltMode())
+          {
+            String label[] = {
+                "The length of the sequence loaded does not match the length of",
+                "the default reference sequence in the BAM ("+seqNames.get(0)+").",
+                (newIndex == -1 ? "" : "The length does match the reference "+
+                    seqNames.get(newIndex)+" so this has been\nset as the default.") 
+            };
+            new NonModalDialog(frame, label);
+          }
         }
       }
     }