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:
Here's the HTML spec on this:
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.