Just embellishing SpliFF's answer, I could fix this problem by adding the following jQuery to my page:
$(function() {
if (jQuery.browser.msie)
$('img[src$=".png"]').each(function() { // must have quotes around .png
this.style.filter = "progid:DXImageTransform.Microsoft.AlphaImageLoader(src="+this.src+",sizingMethod='scale')";
});
});
This will apply the AlphaImageLoader too all PNGs in the page.