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please provide a self running example.

PHP Version 5.1.0-dev, configure with:
'./configure' '--prefix=/usr/' '--with-apxs2' '--with-gettext'
'--with-iconv' '--with-mysql' '--enable-mbstring=ru' '--enable-mbregex'
'--enable-mbstr-enc-trans' '--disable-short-tags' '--with-xsl'
'--with-libxml' '--without-sqlite' '--enable-soap'

libxslt Version 	1.1.8
libxml Version 	2.6.11
libexslt Version 	1.1.8

apache 2.0.48

Reproduce code:
---------------
<?php
final class Menu {
    public static function createXML() {
        $xml = new DomDocument;
        $xml->loadXML('<?xml version="1.0" encoding="iso-8859-1" ?>
        <menus><menu>1</menu><menu>2</menu><menu>3</menu></menus>');
        
        return $xml->saveXML();
    }
}

$xsl = new DomDocument();
$xsl->loadXML(
'<?xml version="1.0" encoding="iso-8859-1" ?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:php="http://php.net/xsl">
<xsl:variable name="menus" select="php:function(\'Menu::createXML\')/menus"/>
<xsl:template match="/">
    <xsl:value-of select="$menus" />
</xsl:template>
</xsl:stylesheet>'
);
    
$xml = new DomDocument;
$xml->loadXML('<?xml version="1.0" encoding="iso-8859-1" ?><null></null>');
    
$proc = new XSLTProcessor();
$proc->registerPhpFunctions();
$proc->importStylesheet($xsl);
    
$dom = $proc->transformToDoc($xml);
echo $dom->saveXML();
?>

Expected result:
----------------
<?xml version="1.0"?>
123

Actual result:
--------------
<br />
<b>Warning</b>:  XSLTProcessor::transformToDoc() [<a href='function.transformToDoc'>function.transformToDoc</a>]: Invalid type in <b>/mnt/data/www/html/linux.grodno.by/web/test.php</b> on line <b>30</b><br />
<br />
<b>Warning</b>:  XSLTProcessor::transformToDoc() [<a href='function.transformToDoc'>function.transformToDoc</a>]: runtime error: file /mnt/data/www/html/linux.grodno.by/web/ element variable in <b>/mnt/data/www/html/linux.grodno.by/web/test.php</b> on line <b>30</b><br />

<br />
<b>Warning</b>:  XSLTProcessor::transformToDoc() [<a href='function.transformToDoc'>function.transformToDoc</a>]: Evaluating global variable   being computed ...  failed in <b>/mnt/data/www/html/linux.grodno.by/web/test.php</b> on line <b>30</b><br />
<?xml version="1.0"?>

I wonder, if that really worked in PHP 5.0.0 ... (doesn't here on 5.0.0-dev)

but change
     return $xml->saveXML();
to
     return $xml;

and it works

(you have to return a DomDocument if you want to access the nodes later...)