I remember mentioning this before, but you must have forgotten about it.
>From what I can see, in all parts of your project you have left
footnotes in your ajax dialogs, instead of converting them to tooltips.
Please find attached a screenshot that shows the difference between one
and the other. If you want to use tooltips (I think it's a good idea),
then you will have to convert the footnotes right after you show your
ajax dialog to the user, the function that does the conversion is called
initTooltips() and it resides inside functions.js. However, after a
quick glance at that function, it looks to me like it needs to be
modified a small bit. Right now it looks for elements across the whole
of the DOM, but it would be better to be able to pass to it an optional
jQuery object as a parameter, so that it is possible to make it look for
footnotes and the respective markers inside a particular object only.
Hope this helps :)