I was having problems using lightbox2 with IE11 on our site. According to this MS forum, the problem is inside lightbox2:

http://social.msdn.microsoft.com/Forums/ie/en-US/c80f75b1-fe8a-4352-ac35...

Here's the relevant bit from that thread:

Lightbox uses browser sniffing....IE11 does not use the MSIE token.
if (Lightbox.alternative_layout) {
$('#bottomNavZoom, #bottomNavZoomOut').css({'bottom': Lightbox.borderSize + 'px', 'right': Lightbox.borderSize + 'px'});
}
else if (Lightbox.rtl == 1 && $.browser.msie) {
$('#bottomNavZoom, #bottomNavZoomOut').css({'left': '0px'});
}

// Force navigation links to always be displayed
if (s.force_show_nav) {
$('#prevLink, #nextLink').addClass("force_show_nav");
}

},