FCKeditor is supposed to output XHTML, but it fails to wrap content of <script> and <style> tags in CDATA sections. This is how a <script> tag should be generated in XHTML:
<script type="text/javascript"> <![CDATA[ var a = "This is a line break: <br/>"; ]]> </script>
Here's the HTML spec on this:
http://www.w3.org/TR/xhtml1/#h-4.8
Lack of CDATA sections screws up any XSLT transformations performed against the generated XHTML.
I would have entered a bug, but your bug tracker is read-only until July 2nd.
Andre