Ok... the line that causes gconftool to bail out is a call to fputs on
line 4030 of markup-tree.c (in the function write_local_schema_info).
Here's the surrounding chunk of code:
  if (write_descs && local_schema->long_desc)
    {
      if (fprintf (f, "%s<longdesc>", whitespace2) < 0)
        goto out;

      s = g_markup_escape_text (local_schema->long_desc, -1);
          
      if (fputs (s, f) < 0)
        {
          g_free (s);
          goto out;
        }
          
      g_free (s);

      if (fputs ("</longdesc>\n", f) < 0)
        goto out;
    }


What's happening is that local_schema->long_desc is an empty string, and fputs 
apparently returns EOF if you pass it an empty string.

So now the question becomes what changed that caused this code to get
run even if long_desc is an empty string?

-- 
update-schemas: Error writing file 
"/var/lib/gconf/defaults/%gconf-tree.xml.new": File exists
https://launchpad.net/bugs/74699

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