Perhaps the issue is due to the scrollbars being included in the width and height regardless of whether or not they are there. I don't have IE (on a mac) so can't verify.

However, I can tell you what does work as in my project jQuery Lightbox I have no such issue. We use the following code in it:

// Make the overlay the size of the body

var $body = $(this.ie6 ? document.body : document); // using document in ie6 causes a crash

$('#lightbox-overlay').css({

 width:  $body.width(),

 height:  $body.height()

});



// ... some code ...



// Get the window dimensions

var $window = $(window);

var wWidth  = $window.width();

var wHeight = $window.height();

And the overlay displays correctly. I would trust jQuery's result of the width and height compared to that of the native result, as jQuery should naturally be taking into account any quirks with the browser.

It is important to note that the lightbox script above tends to prefer $(document) over $(document.body) for some reason - I can't remember sorry :O - so perhaps this solves the issue as well?