Is this really a Windows problem?
This code, which you will need to modify slightly should work.
<script type="text/javascript">
var opener;
function windowopen()
{
opener = window.open('test.html', 'test', 'width=400;height=200;');
}
function windowclose()
{
opener.window.close();
}
</script>
I just used 2 links on the parent from like this
<a href="#" onclick="windowopen();">Open</a> <a href="#" onclick="windowclose();">Close</a>
As you can tryout, it should close the opened window from the parent.