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The only way to solve all the JSON Bugs is to offer CKEditor for JQuery not CKEditor, I don't know why we are not using the JQuery version in the first place seeming JQuery is part of xoops.
Without CKEditor for JQuery there is no way and we have not offered any single editor that works for example with JSON and JQuery or any other functions of JQuery.
Kris could you consider using CKEditor for JQuery instead you can get it off their main site there is a link at the bottom for it.