1. Sun officially acknowledged that this is a bug (see below). It also
appears in jre version 1.6.

2. I have a workaround (see far below). With this workaround the
wrapping behavior seems to work like it used to even on new versions
of the JRE.

************************ From Sun ******************************

Hi Reinhard Engels,

Thank you for reporting this issue.

We have determined that this report is a new bug and entered the bug
into our internal bug tracking system under Bug Id: 6539700.

You can monitor this bug on the Java Bug Database at
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6539700.

It may take a day or two before your bug shows up in this external
database. As you are a member of the Sun Developer Network (SDN),
there are two additional options once the bug is visible.

1. Voting for the bug
  Click http://bugs.sun.com/bugdatabase/addVote.do?bug_id=6539700.

2. Adding the report to your Bug Watch list.
  You will receive an email notification when this bug is updated.
  Click http://bugs.sun.com/bugdatabase/addBugWatch.do?bug_id=6539700.

SDN members can obtain fully licensed Java IDEs for web and enterprise
development.  More information is at http://developers.sun.com/prodtech/javatools/free/.

We greatly appreciate your efforts in identifying areas in the J2SE
where we can improve upon and I would request you to continue doing
so.

************************ End From Sun ******************************

************************ The workaround (same code as previously
posted, plus an (inner) subclass of StyledEditorKit) ************

import java.awt.Color;
import java.awt.Font;

import javax.swing.JFrame;
import javax.swing.JScrollPane;
import javax.swing.JTextPane;
import javax.swing.text.AbstractDocument;
import javax.swing.text.BadLocationException;
import javax.swing.text.BoxView;
import javax.swing.text.ComponentView;
import javax.swing.text.Document;
import javax.swing.text.Element;
import javax.swing.text.IconView;
import javax.swing.text.LabelView;
import javax.swing.text.MutableAttributeSet;
import javax.swing.text.ParagraphView;
import javax.swing.text.SimpleAttributeSet;
import javax.swing.text.StyleConstants;
import javax.swing.text.StyledEditorKit;
import javax.swing.text.View;
import javax.swing.text.ViewFactory;

public class JTextPaneWrapChangeDemo {

   public JTextPaneWrapChangeDemo() {
       super();
   }

   public static void main(String[] args) {
       JTextPaneWrapChangeDemo demo = new JTextPaneWrapChangeDemo();
       demo.run();
   }

   public void run() {
       JFrame frame = new JFrame();
       frame.setSize(400, 400);
       frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
       JTextPane textPane = new JTextPane();
       JScrollPane scrollPane = new JScrollPane(textPane);
       frame.add(scrollPane);
       textPane.setEditable(false);
       textPane.setEditorKit(new BioSequenceStyledEditorKit());
       textPane.setFont(new Font("Courier", Font.PLAIN, 12));
       MutableAttributeSet exonAttributeSet = new
SimpleAttributeSet();
       MutableAttributeSet intronAttributeSet = new
SimpleAttributeSet();
       StyleConstants.setFontSize(exonAttributeSet, 12);
       StyleConstants.setForeground(exonAttributeSet, Color.blue);
       StyleConstants.setFontSize(intronAttributeSet, 12);
       StyleConstants.setForeground(intronAttributeSet, Color.black);
       try {
           Document d = textPane.getDocument();
           d.insertString(d.getLength(), exon1, exonAttributeSet);
           d.insertString(d.getLength(), intron1,
intronAttributeSet);
           d.insertString(d.getLength(), exon2, exonAttributeSet);
           d.insertString(d.getLength(), intron2,
intronAttributeSet);
           d.insertString(d.getLength(), exon3, exonAttributeSet);

       } catch (BadLocationException e) {
           System.out.println("bad location exception" + e);
       }
       frame.show();
   }

   String exon1 =
"ATGCCACCAAAAGCGCGTATAAACTCAAAAAATTCAGTTGAGCAGGAGGGAAGGGTCCTACTTGCAGTATCAGCTTTGAAAAATAAGGAAATTCTCAATATTCGTGAAGCTGCGCGTGTCTATAATGTGCCTTATACTACCCTCCAGCGGCGCCTAAAGGGGCATACTTTTCGAGCTGAATTACGCGCAAATGGCCATAAAATGACTCAGAATGAAGAGGATTCACTTATTAGATGGATTCTATCTATGGATCAACGTGGAGCGGCTCCCCGACCGTCCCATGTACGAGAAATGGCGAATATCCTGCTTGCGCAGCGTGGTTCAACTCCTACCCAGACTGTTGGAGAGAAATGGGTATATAACTTCATTAATCGGCATGATGAGATCAAAACCCGATTCTCTAGGCGCTATAACCACCAGCGTGCTAAATGTGAAGACCCAAAGATTATCCTGGAATGGTTCAATCGTGTCCAGATCACAATAATGCAGCATGGGATTACACTGGAAGATATCTACAACTTTGATGAAACTGGCTTTGCAATGGGCTTAGTAGCTACTGCTAAG";
   String intron1 =
"GTAGTTACAAGAGCTGAGATGCTTAGTCGGCCCTTCCTTATCCAGCCAGGGAACCGCGAATGGGTTACCTCTATAGAGTGTATTAACTCTACTGGCTGGGTGCTTCCACCATGCATTATCTTCAAGGGAAAGGTCCATATTGAGGACTGGTATTAAGATACAGCCTTACCAGCAGACTGGCGGATCGAGGTCAGTGAGAATGGATGGACGACTGATCAGATTGGATTACGATGGCTTCAAAAAGTCTTTATTCCTGCTACTACCAGTCGTACAACTGGTAGATATCGACTATTAATTCTTGATGGCCATGGGAGCCATCTAACACCACAGTTTGATCAAATCTGCACTGAGAATGATATCATTCCAATCTGCATGCCTGCACATTCATCACATCTCCTCCAGCCTCTAGATGTTGGCTGTTTCTCTCCTCTTAAGCGTGCGTATGGCCGCTTGATTGAGGATAAGATGCGGCTTGGTTTCAACCATATTGACAAGTTTGATTTCCTTGAGGCCTATCCACAAGCTCATACGGCAATCTTTTCAGCAGATAATATTAAAAGTGGCTTTTCAGCAACTGGATTAATACCACTGAATCCAGATCGGGTGCTCAGTCAGCTTAATATCCAGCTTAGAACACCTACACCACCAGGCAGCCGATCAACTAATTCTGTCCCAAAAACACCTTACAATCTCAAGCA";
   String exon2 =
"GCTGAAGAAGCAGGAAACTACGCTTAAGAAGCTACTTAGGGAGCGTACATACAGCCCTCCTACCCCTACAAAGGCTGTGCTAGGTCAGATTATCAAGGGGTGTGAGATGGCAATGAATAACGCTGCCCTTCTTGCAAAGGAAAATCATGATCTACGTGCTGCACATGAAAAGCACCTTCAAAAGCAGAAGCGATCTAGGCGGCAGATAGAAACTGCA";
   String intron2 =
"GTGGGATTATCTATCCAGGAAGGGCAGGAGATCATTTAACGCAGGGATCAGGCTGCTGAAGCTATCCCAACTATCCCTCCAGAGCAGGTAGTAGATACAGAACAACGCCCTCAACGGGCACCCCCACGCTGCAGTGACTGCCATATTCTAGGCCATAGGCGATTGCAATGTCCGCAGCGCAAGAATAACTAGATTTAGTAATAAAATCATGTTTTAGGGGTTCAAAATAGCCTCCAATTTCGGCCGCGGCCAAATTCTATAG";
   String exon3 =
"TATGGTGATCCGCTCGGTTACGTGATCCGCTCGCTTACCGATTACGTTACTTCTCTGGAAGACGATCCTGGACTAAGTCATTTCCTTTTGCGTAGTTCAGCGGATTTTTTTTTTCTTCTGCTACTTGGGGTCGCTGAAGATGGAATCAATCAGACGT";

   class BioSequenceStyledEditorKit extends StyledEditorKit {

       ViewFactory defaultFactory = new WrapColumnFactory();

       public ViewFactory getViewFactory() {
           return defaultFactory;
       }

       public BioSequenceStyledEditorKit() {
           super();
       }

       class BioSequenceLabelView extends LabelView {
           public BioSequenceLabelView(Element elem) {
               super(elem);
           }

           public int getBreakWeight(int axis, float pos, float len)
{
               if (axis == View.X_AXIS) {
                   checkPainter();
                   int p0 = getStartOffset();
                   int p1 =
getGlyphPainter().getBoundedPosition(this, p0,
                           pos, len);
                   if (p1 == p0) {
                       // can't even fit a single character
                       return View.BadBreakWeight;
                   }
                   // if (getBreakSpot(p0, p1) != -1) {
                   // return View.ExcellentBreakWeight;
                   // }
                   // Nothing good to break on.
                   return View.GoodBreakWeight;
               }
               return super.getBreakWeight(axis, pos, len);
           }
       }

       class WrapColumnFactory implements ViewFactory {
           public View create(Element elem) {
               String kind = elem.getName();
               if (kind != null) {
                   if
(kind.equals(AbstractDocument.ContentElementName)) {
                       return new BioSequenceLabelView(elem);
                   } else if (kind
                           .equals(AbstractDocument.ParagraphElementName))
{
                       return new ParagraphView(elem);
                   } else if
(kind.equals(AbstractDocument.SectionElementName)) {
                       return new BoxView(elem, View.Y_AXIS);
                   } else if
(kind.equals(StyleConstants.ComponentElementName)) {
                       return new ComponentView(elem);
                   } else if
(kind.equals(StyleConstants.IconElementName)) {
                       return new IconView(elem);
                   }
               }
               return new LabelView(elem);
           }
       }

   }

}