I have two anchors positioned absolute on top of an image, the links are clickable in other browsers (Chrome, FF, Safari) but not in IE (tested in 8 & 9 so far)
@tw16's comment mentioning invisible got me thinking about opacity.
Combining IE's filter:alpha(opacity=0) with background-color:#fff (or any color) appears to be a good solution for this. Tested and works in IE 7-9 (6 isn't applying the opacity filter for some reason but I'm not required to support 6 so this will work)
The 1x1 image solution is globally effect so I'm going to give the check to him.
Thanks for the answers.