The script below lists files in the current directory, which are mrtg html and image output files.  The directory listing is parsed for the host name and a row for each host is rendered with traffic, cpu, and uptime html and image files on the corresponding row.  
Prior to upgrading from 4.0.6 to 4.2.2 the following script produced correct output.  After upgrading, multiple rows for each host are output in no specific order.  Here's the broken application:
http://tempe.dedserius.com/mrtg/

I took the application to an i386 server configured identically and tested it and it worked fine:
http://winslow.dedserius.com/mrtg/
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<table align="center" border=0 width="80%">
<%
    $handle=opendir('.');
    $colcount=0;
%>
  <tr bgcolor="#cccccc">
    <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica"><STRONG>Host</STRONG><!--mstheme--></font></td>
    <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica"><STRONG>Traffic</STRONG><!--mstheme--></font></td>
    <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica"><STRONG>CPU</STRONG><!--mstheme--></font></td>
    <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica"><STRONG>Uptime</STRONG><!--mstheme--></font></td>
  </tr>
<%
    while ($file = readdir($handle))
    {
    // Get the host name
    $host = substr($file,0,strpos($file,"."));
    if ( $host == "why" || $host == "cisco" || $host == "winslow"
      || $host == "yuma" || $host == "sedona"
      || $host == "tempe" || $host == "scottsdale"
      || $host == "vanboers" || $host == "sedonant" )
    {
      if ($host != $tmphost )
      {
        $i++;
        $fArray[$i] = array(
          "host"=>"$host");
      }
    $tmphost = $host;
    }
  }
  sort($fArray);
  closedir($handle);
  $cnt=0;
  for ($j=0; $j < count($fArray); $j++)
  {
    if ($fArray[$j][host] != $fArray[$j-1][host])
    {
      if ( ($cnt/2) == round($cnt/2))
      {
        $bgcolor="#ccccff";
      } else {
        $bgcolor="#ccddff";
      }
      echo "<tr bgcolor=\"$bgcolor\">\n";
      echo "<td><b>".$j." | ".ucfirst($fArray[$j][host])."</b></td>\n";
      switch ($fArray[$j][host])
      {
        case "why";
          echo "<td align=\"center\"><a href=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth0.pub.html\">";
          echo "<img src=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth0.pub-day.png\" border=0
            alt=\"".$fArray[$j][host]." Daily Public Traffic\" width=\"100\" height=\"50\"></a>&nbsp;";
          echo "<a href=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth1.priv.html\">";
          echo "<img src=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth1.priv-day.png\" border=0
            alt=\"".$fArray[$j][host]." Daily Private Traffic\" width=\"100\" height=\"50\"></a>";
          echo "</td>";
          break;
        case "cisco";
          echo "<td align=\"center\"><a href=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth0.html\">";
          echo "<img src=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth0-day.png\" border=0
            alt=\"".$fArray[$j][host]." Daily Private Traffic\" width=\"100\" height=\"50\"></a>&nbsp;";
          echo "<a href=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".ppp0.html\">";
          echo "<img src=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".ppp0-day.png\" border=0
            alt=\"".$fArray[$j][host]." Daily Public Traffic\" width=\"100\" height=\"50\"></a>";
          echo "</td>";
          break;
        default;
          echo "<td align=\"center\"><a href=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth0.html\">";
          echo "<img src=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".eth0-day.png\" border=0
            alt=\"".$fArray[$j][host]." Daily Traffic\" width=\"200\" height=\"50\"></a></td>";
          break;
      }
      echo "<td align=\"center\"><a href=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".cpu.html\">";
                  echo "<img src=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".cpu-day.png\" border=0
        alt=\"".$fArray[$j][host]." Daily CPU\" width=\"200\" height=\"50\"></a></td>";
      echo "<td align=\"center\"><a href=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".uptime.html\">";
      echo "<img src=\"http://".$HTTP_HOST."/mrtg/".$fArray[$j][host].".uptime-month.png\" border=0
         alt=\"".$fArray[$j][host]." Daily Uptime\" width=\"200\" height=\"50\"></a></td>";
      echo "</tr>\n";
      $cnt++;
    }
}
%>
        <tr bgcolor="#cccccc">
                <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica">
      <STRONG>All</STRONG><!--mstheme--></font></td>
                <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica">
      <STRONG><a href="http://<% echo $HTTP_HOST."/mrtg/"%>all.traffic.html">Traffic</a></STRONG><!--mstheme--></font></td>
                <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica">
      <STRONG><a href="http://<% echo $HTTP_HOST."/mrtg/"%>all.cpu.html">CPU</a></STRONG><!--mstheme--></font></td>
                <td align=center><!--mstheme--><font face="Century Gothic, Arial, Helvetica">
      <STRONG><a href="http://<% echo $HTTP_HOST."/mrtg/"%>all.uptime.html">Uptime</a></STRONG><!--mstheme--></font></td>
        </tr>
<%
  echo "</table>";
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./configure --with-apache=/usr/src/apache_1.3.26 --with-mysql=/usr/local --with-gd=/usr/gd1.3 --with-snmp --enable-ucd-snmp-hack