Susan, I am committing a patch for this momentarily ... along with the full relase version of Scriptaculous/Prototype, Adam.
If you want to test early, in the document.parser.class.inc.php file, search for two instances of:
$this->documentContent = preg_replace("/(<head[^>]*>)/i", "\\1\n".$js, $this->documentContent);
and replace with:
$this->documentContent = preg_replace("/(<\/head>)/i", $js."\n\\1", $this->documentContent);