Just in case if there is anybody still struggling with this problem (I’m sure there is). I hate the very idea of writing a code, especially to solve such a trivial problem. The easiest and 100% effective way is to save your doc or docx file as rtf. Now place the newborn rtf file into your publication using whatever way (I prefer drag and drop), and voila! The naughty text appears with all the footnotes right in their places, no crossed squares and pink spots any more.

BTW: my setup is Win7/CS6, but I don’t think that this combination has any special advantages.