Thank you for this bug report. To properly diagnose the problem, we
need a short but complete example script to be able to reproduce
this bug ourselves. 

A proper reproducing script starts with <?php and ends with ?>,
is max. 10-20 lines long and does not require any external 
resources such as databases, etc. If the script requires a 
database to demonstrate the issue, please make sure it creates 
all necessary tables, stored procedures etc.

Please avoid embedding huge scripts into the report.

--

I get the correct (expected) behavior using

<?php

$xml = <<<XML
<root><node1><node2>empty</node2></node1></root>
XML;

$dom = new DOMDocument("1.0", "iso-8859-2");
$dom->loadXML($xml);

$dom = new DOMDocument("1.0", "iso-8859-2");
$dom->loadXML($xml);

$node1 = $dom->getElementsByTagName("node1")->item(0);
$node1->getElementsByTagName("node2")->item(0)->nodeValue = "full";

echo $dom->saveXML();
// <root><node1><node2>full</node2></node1></root>

?>

<?php
//the entire code's language is Hungarian, please excuse me for the funny mixture of the English and Hungarian
define("max_mail",10);
define("CrLf","\r\n");
define("Cr","\n");

//link for the xml file: http://paskal-bt.hu/bakny
$xml_file = "http://paskal-bt.hu/bakny/PHP-cimlista-proba.xml";
$xml_sablon = "http://paskal-bt.hu/bakny/PHP-xml_sablon.php";

$dom = new DOMDocument('1.0', 'iso-8859-2');
if (!file_exists($xml_file)) {
$dom->loadXML($xml_sablon);
$dom->save($xml_file);
} //if f_exists 
else {
$dom->load($xml_file);
}	//else
$cimlista = $dom->getElementsByTagName('Cimlista');
$napi_mail_szam = 0;

$dom = new DOMDocument('1.0', 'ISO-8859-2');	//this is the second instanciateting of the $dom object
if (!$dom->load($xml_file)) {
  echo "Error while parsing the document: $xml_file\n";
  exit;
}

$dom->formatOutput = true;

$items = $dom->getElementsByTagName('E-mail');
for ($i=0; $i < $items->length ; $i++) {
$mail_items_tomb[$i] = $items->item($i)->nodeValue;
}//for i

$items = $dom->getElementsByTagName('Elkuldve');
for ($i=0; $i < $items->length ; $i++) {
$elkuldve_items_tomb[$i] = $items->item($i)->nodeValue;
}//for i
$i = 0;	$tomb_meret = count($mail_items_tomb);
$elkuldve_valasz = "1";

while ($i < $tomb_meret)  {
$akt_elem = $cimlista->item($i);

$siker = true;	//in the entire PHP code $siker is the result of a mail() function. For the 20 lines maximum code-size I deleted all the lines, which are unrelevants.
if ($siker) {
$akt_elem->getElementsByTagName('Elkuldve')->item(0)->nodeValue = $elkuldve_valasz;
echo $akt_elem->getElementsByTagName('Elkuldve')->item(0)->nodeValue;	//this line is not in the entire code, I inserted only for demonstrating the bug.
}	//if siker
++$i;
}	//while vége
$dom->saveXML();//this line is not in the entire code, I inserted only for demonstrating the bug.
$dom->normalize;
//$dom->save($xml_file);	//the entire code save the new xml database file here. I commented out this line only for the PHP demonstration.
echo "Az eredmény mentve";
?>

$xml_file = "http://paskal-bt.hu/bakny/PHP-cimlista-proba.xml";
$dom->save($xml_file);

You cannot save to a file over the internet. Change $xml_file to be a local file path, and a file path that your script has write access to. Any change in behavior?

How can I send the xml files? I can't see any form-field, or button for sending or upload files? Is it good the "Add a Patch" button? T'm gona to send on that. Please delete the first line, than rename that as xml.

That's not what I'm talking about.

Please find a mailing list or forum to get further help with your script. In the mean time I'm still quite sure this isn't a bug with PHP but with your code instead.
http://www.php.net/support.php