Run the following program using JDK 6 b102 on Unix after adding saxon8.jar (unpacked from http://prdownloads.sourceforge.net/saxon/saxonb8-8j.zip?download) to the classpath:

---%<---
import java.util.prefs.BackingStoreException;
import java.util.prefs.Preferences;
public class IndentNumberBug {
    public static void main(String[] args) throws BackingStoreException {
        Preferences p = Preferences.userRoot().node("test/node");
        p.removeNode();
        p = Preferences.userRoot().node("test/node");
        p.put("k", "v");
        p.flush();
    }
}
---%<---

You will see:

---%<---
Exception in thread "main" java.util.prefs.BackingStoreException: java.lang.IllegalArgumentException: Unknown attribute indent-number
        at java.util.prefs.FileSystemPreferences$8.run(FileSystemPreferences.java:615)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.util.prefs.FileSystemPreferences.writeBackCache(FileSystemPreferences.java:600)
        at java.util.prefs.FileSystemPreferences.syncSpiPrivileged(FileSystemPreferences.java:784)
        at java.util.prefs.FileSystemPreferences.access$2300(FileSystemPreferences.java:33)
        at java.util.prefs.FileSystemPreferences$13.run(FileSystemPreferences.java:754)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.util.prefs.FileSystemPreferences.syncSpi(FileSystemPreferences.java:752)
        at java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1317)
        at java.util.prefs.AbstractPreferences.sync(AbstractPreferences.java:1308)
        at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:731)
        at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:807)
        at IndentNumberBug.main(IndentNumberBug.java:9)
Caused by: java.lang.IllegalArgumentException: Unknown attribute indent-number
        at net.sf.saxon.Configuration.setConfigurationProperty(Configuration.java:2260)
        at net.sf.saxon.TransformerFactoryImpl.setAttribute(TransformerFactoryImpl.java:342)
        at java.util.prefs.XmlSupport.writeDoc(XmlSupport.java:247)
        at java.util.prefs.XmlSupport.exportMap(XmlSupport.java:333)
        at java.util.prefs.FileSystemPreferences$8.run(FileSystemPreferences.java:607)
        ... 12 more
Oct 25, 2006 3:29:13 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: java.lang.IllegalArgumentException: Unknown attribute indent-number
---%<---

Worse, if you comment out the call to flush(), you get an unhelpful message (took me a while to track this down to its source!) and no stack trace:

---%<---
Oct 25, 2006 3:34:43 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: java.lang.IllegalArgumentException: Unknown attribute indent-number
---%<---