I use the following snip of a script:
if ($.browser.msie && $.browser.version < 9) { extra = \"?\" + Math.floor(Math.random() * 3000); }
I had this problem as well. We were using two versions of Jquery (1.11.3 and 1.8.3), one of which was causing this issue. I found a lightbox_me.js release that worked on both versions:
http://buckwilson.me/lightboxme/
It was just an easy replacement of an old file.