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.

here sample code that can reproduce the problem

class DOMDocument_NIC extends DOMDocument{   
    public function isValid_onfile(){
        $tempFile = time() . '-' . rand() . '-xmlvalidation.tmp';
        $this->save($tempFile);
     
        // Create temporary DOMDocument_NIC and re-load content from file.
        $tempDom = new DOMDocument();
        $tempDom->load($tempFile);
     
        // Delete temporary file.
        if (is_file($tempFile)){
            unlink($tempFile);
        }
        return $tempDom->schemaValidate('hosting_epp_nic_it/epp-1.0.xsd');
    }
    public function isValid_onfly(){
        return $this->schemaValidate('hosting_epp_nic_it/epp-1.0.xsd');
    }
}


$doc = new DOMDocument_NIC('1.0', 'UTF-8');
$doc->xmlStandalone='no';
$xml_epp = $doc->createElementNS("urn:ietf:params:xml:ns:epp-1.0",'epp');
$doc->appendChild($xml_epp);
$xml_epp->setAttributeNS('http://www.w3.org/2000/xmlns/' ,'xmlns:xsi', 
'http://www.w3.org/2001/XMLSchema-instance');
$xml_epp->setAttributeNS('http://www.w3.org/2001/XMLSchema-instance' 
,'xsi:schemaLocation', 'urn:ietf:params:xml:ns:epp-1.0 epp-1.0.xsd');   
$xml_command = $doc->createElement('command');
$xml_epp->appendChild($xml_command);
$xml_login = $doc->createElement('logout');
$xml_command->appendChild($xml_login);
$xml_cltrid = $doc->createElement('clTRID',"123456");
$xml_command->appendChild($xml_cltrid);

//$response = new DOMDocument_NIC();
//$response->loadXML($xml);
echo htmlentities($doc->saveXML())."<br />";
echo "Valido on File: ".$doc->isValid_onfile();
echo "Valido on Fly: ".$doc->isValid_onfly();

Thank you for taking the time to write to us, but this is not
a bug. Please double-check the documentation available at
http://www.php.net/manual/ and the instructions on how to report
a bug at http://bugs.php.net/how-to-report.php

createElement is level 1 non-namespace aware method. Use level 2 
createElementNS method for all elements and create them in the 
urn:ietf:params:xml:ns:epp-1.0 namespace.