jQuery NEEDS <!DOCTYPE HTML> in order to render $(window).height() properly. $(window).height() is what ColorBox uses to determine the vertical center of the view-port. If <!DOCTYPE HTML> isn’t present $(window).height() is equal to $(document).height() which is NOT what you want to have happening on pages that scroll.
Add <!DOCTYPE HTML> as the first line above that <html <?php language_attributes(); ?>> tag and see if that helps.
i.e.:
<!DOCTYPE HTML>
<html <?php language_attributes(); ?>>
