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Either allow for the size taken up by toolbars in Internet Explorer when specifying the width and height to the window:
<script language="JavaScript"><!-- if (nagiator.appName=='Internet Explorer') var width=100,height=150; else var width=100,height=100; window.open('about.blank','windowName','width=' + width + ',height=' + height); //--></script>
Or from within the the popup window, resize it to the size you require:
<script language="JavaScript"><!-- if (document.all) window.resizeTo(100,150); else if (document.layers) window.resizeTo(100,100); } //--></script>