If you are using sticky footers (ATO->Style & edit FOOTER->Sticky footer on short pages?) AND are using full width headers (ATO->Style & edit HEADER AREA->Full Width Header) The footer will be pushed below the bottom of the viewers window.

To fix this problem you can eithor (1) edit js.php and change line 280-281 from

	var headerheight = jQuery("td#header").height();
	var footerheight = jQuery("td#footer").height();

to

	var headerheight = jQuery("td#header").height() + jQuery("div#header").height();
	var footerheight = jQuery("td#footer").height() + jQuery("div#footer").height();

or (2) download the attached file, unzip it and replace js.php with the fixed version.

Unchecking the full-width header option this issue remains. But unchecking full-width footer solves it. (Even without your suggested modifications).

Edit: Oops, it seemed like it did solve it. But I was wrong, sorry.