It's a feature by design.
When you are using Javascripts, CuteEditor will enclose it within the starting tag <![CDATA[ and the ending tag ]]>.
This will mark it as unparsed character data. Otherwise characters like & and < will be treated as start of character entities (like ) and tags (like <b>) respectively.
Example for XHTML BLOCKED SCRIPT
<script type="text/javascript" language="Javascript">
<!--
<![CDATA[
document.write('Hello World!');
]]>
//-->
</script>
XHTML and Stylesheets
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