AAP,
Have you set Editor.EditCompleteDocument Property to true?
Editor.EditCompleteDocument Property
Specify whether a complete HTML document is being edited.
public
bool EditCompleteDocument {get; set;}
Remarks
If false, the editor will only process content inside the page body i.e. all content inside of the <body>...</body> tags of a page. If true, the editor will process content outside the page body and preserve header tags (e.g. <head>...</head>, <title>...</title>, etc.).
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