IE is essentially ignoring the z-index of absolutely positioned elements (see: http://stackoverflow.com/questions/11380117/cant-click-div-with-links-behind-another-div-absolute-position-wont-work), which I guess it shouldn't be doing, but is.
Based on what I've read there's no real workaround for this specific situation, because we need both elements (the slides and the dots) to be clickable, which leaves two options. Rework the php to position the control-nav container before the slides container, which would allow positioning the control-nav container at the top of the image, or leave the control-nav container at the bottom of the image.