I am using jquery dialogs to present forms (fetched via AJAX). On some forms I am using a CKEditor for the textareas. The editor displays fine on the first load.
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I've had similar issue where we were making several instances of CKeditor for the content loaded via ajax.
CKEDITOR.remove()
Kept the DOM in the memory and didn't remove all the bindings.
CKEDITOR.instance[instance_id].destroy()
Gave the error i.contentWindow error whenever I create new instance with new data from ajax. But this was only until I figured out that I was destroying the instance after clearing the DOM.
Use destroy() while the instance & it's DOM is present on the page, then it works perfectly fine.