At this point I resolved the problem, it lies somewhere in between the original release and the one I downloaded a few day ago. I was able to restore the editor back to the original state where it was sort of working, and add the new files until i resolved the problem.
If i have time i will try and recreate the problem on a new dummy site this weekend. I cannot afford to shut down my client again. There is also a problem with XML creation, you are not by default using 4.0 xml (Check include_cuteeditor.asp if you do not belive me) as Adam stated in a previous thread.
I do modify the include_cuteeditor.asp, winie.js, winie.js.asp and gecko.js.asp. The nature of my application has the editor residing inside iframe, when the user resizes the editor your application does not have any event to indicate this. I added one just as i had to add a new property to the editor text area to allow a class to be applied, you allow a style, but not a class.
You also seem un under utilize the XML configuration files, as I posted earler on a three line fix to add variable widths to the drop down menus.
Modifing the three js files by the way is, well not fun