Sono riuscito a farlo funzionare solo in questo modo, collaudato con IE6 e NN6
codice:
<%@ Language=VBScript %>
<HTML>
<HEAD>
<META NAME="GENERATOR" Content="Microsoft Visual Studio 6.0">
<SCRIPT ID=clientEventHandlersJS LANGUAGE=javascript>
<!--
var w = null;
function button1_onclick() {
	w = window.open("pupup_frame.asp", "popup","width=300,height=300,");
	window.setTimeout("ha_frames()", 0);
}

function ha_frames()
{
	alert(w.window.frames.length);
}
//-->
</SCRIPT>
</HEAD>
<BODY>

<h1>a.asp</h1>
<INPUT type="button" value="Button" id=button1 name=button1 
LANGUAGE=javascript onclick="return button1_onclick()">

</BODY>
</HTML>