Hi Chris,
It certainly looks from this end as though it is the infowindow shadow pane that is causing the problem in IE.
Test it out by adding a line to your wagmp_map_1.php. (the number of your instance of your map might be different)
Find the block of code under and including the line similar to:
function wagmp_map_1() {
Place your cursor at the end of the last line in that block, press 'return' to start a new line, and paste in:
map.getPane(G_MAP_FLOAT_SHADOW_PANE).style.visibility="hidden";
In my file it would be like this:
function wagmp_map_1() {
if(GBrowserIsCompatible()) {
if(!document.getElementById('wagmp_map_1')) return false;
var map = new GMap2(document.getElementById('wagmp_map_1'));
wagmp_map_1_obj = new WAMapRef(map);
map.enableContinuousZoom();
map.enableDoubleClickZoom();
map.addControl(new GSmallMapControl());
map.addControl(new GMapTypeControl());
var geocoder = new GClientGeocoder();
map.getPane(G_MAP_FLOAT_SHADOW_PANE).style.visibility="hidden";
This doesn't give you a functioning shadow effect, but it might be better to have no shadow until someone posts a good solution. If nothing else it might help the diagnostic process!