Looks like you are still firing the base code after the IE code. If all you wish to change is the opacity then do this:
<script type="text/javascript">
opacity = 0.9;
</script>
<!--[if IE]>
<script type="text/javascript">
opacity = 0.1;
</script>
<![endif]-->
<script>
$(document).ready(function () {
$('#usa').mapster({
fillOpacity: opacity,
render_highlight: {
fillColor: '2aff00',
stroke: false,
altImage: 'theImages/skillsets.png'
},
render_select: {
fillColor: 'ff000c',
stroke: false,
altImage: 'theImages/skillsets.png'
},
fadeInterval: 50
});
});
</script>