Has anyone encountered problems with Word footnotes?

I've let go of MS Word and the Office suite completely so I wouldn't know.
You'll probably get a better answer over at the CKEditor forum.

Cleaning up after all the permutations of Windows/Mac, Office/Works and browsers is a nightmare and I'm honestly surprised that the developers of the more popular editors go to such lengths to try. The open source alternatives aren't much better in many cases though...

What actually goes into the editor depends on several steps. First, there's what the program you're copying from decides to put in the clipboard. Everything cut or copied can have alternate versions in the clipboard. The clipboard could contain a fragment of an actual MS Word document, an "HTML" version, a rich-text version, a plain text version and so on. Next, the browser must decide which one of these versions is pasted to the document. Textareas get plain text, divs/iframes with content-editable get the "HTML", and so on. Then, it's up to the editor how it processes the contents before adding it to the document. Lastly, the browser gets another shot at modifying the DOM to its likings.

I can't tell you where in all this things go wrong, but if you're familiar with a JavaScript debugger like Firebug - or the browser's builtin tools - putting a few breakpoints in the editor's paste-plugin should be enough to determine what actually gets pasted, and them move on from there...

Sorry for the pessimism... ;)

Closing this to clean up the queue.