So I noticed a display issue with the transparent background of the MB_overlay. Essentially, in ie9 this background would not show up like it did with all other browsers (firefox, chrome, ie8). I found a fix which basically involved removing one of the inline style settings in the .js file.
Find the line
this.MBoverlay = new Element("div", {id: "MB_overlay", style: "opacity: 0"});
and replace with
this.MBoverlay = new Element("div", {id: "MB_overlay"});
and it seems to do the trick.