Not sure exactly what you are experiencing, but I have successfully stored data on the opener from the child popup on a regular basis in IE (6,7 & 8) in development and production applications.
do you have a URL or some more source code that you can provide?
on a related note... you aren't trying to determine the type of an object on the opener... from the popup are you? - there's some known IE bugs in this area.
Update:
Here's a quick example...
<!--main window-->
<script>
function getThing(id){
url = 'http://mysite.com/...whatever...';
features = 'locationbar=X,menubar=Y...';
window['popup4'+id] = open(url, 'someNameWithoutSpaces', features);
}
function popupCallback(data){
alert('I got data back! ' + data);
document.getElementById('someID').innerHTML = '<b>' + data.label + ' (' + data.id + ')</b>';
//close the popup (now that we have/are done with the data)
window['popup4someID'].close();
}
</script>
<div id="someID">{Nothing Selected Yet}</div>
<input type="button" value="Pick One" onclick="getThing('someID');"/>
<!--popup window-->
<script>
function saveSelection(){
//acquire data however you want/need
var selData = {};
selData.id = 123456;
selData.label = 'iPod Touch (Jeff Atwood Edition)';
//call callback on opener
window.opener.popupCallback(selData);
}
</script>
Update 2
In testing it appears that in IE7,IE8 (but not IE6) after the popup window is closed, any reference data is lost (the references don't capture a snapshot) thus if you need the data after the popup is closed, you will need to clone it.
I thought if the data can be wrapped in an Array, cloning is a piece of cake. Just call .slice() on it to copy it, but... that doesn't work either!
I guess you'll need to save the values out that you need (either to form elements, or the DOM) since IE doesn't look like it will let you use them after the popup closes. :-(