jonathanexact,
Yes, CleanUpHTMLCode will encase script code with a CDATA block. CleanUpHTMLCode() converts html code into xhtml code first. A CDATA section is required in XHTML.
If you do need to remove CDATA block, you can use the following method:
string mytest = EditorUtility.CleanUpHTMLCode(Editor1.Text);
Hope it helps.
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