I am writing a site using jquery that repeatedly calls $(window).width() and $(window).height() to position and size elements based on the viewport
$(window).width()
$(window).height()
I think what you're seeing is the hiding and showing of scrollbars. Here's a quick demo showing the width change.
As an aside: do you need to poll constantly? You might be able to optimize your code to run on the resize event, like this:
$(window).resize(function() { //update stuff });