What tyoe of popups are you referring to? Is it you have
images in separate topics to which you link to via a popup
hyperlink? If so, they will only be included in the printed
document if you specify them in the TOC step of the SSL wizzard.
Even then, they won't appear at the point of the hyperlink. What
you could do is create a book at the bottom of your TOC called
"Popups", add all your popup topics to it and then generate the
word doc. If you wanted, you could manually move the relevant popup
to the required point in the document.