Problem with PopUp Windows and Frames

I have a simple frameset that loads two separate files, one on the fly - cgi created, top and bottom. The popup window script is in the frames window (index.htm) and appears, then immediately layers under the browser window after the "on-the-fly" frame contents are loaded. I can make it re-appear by using the following script:
var timer = '';
function blurred() {
timer = setTimeout('self.focus()',20000);
}

function focused() {
if (timer != '')
clearTimeout(timer);
}
//-->

but I don't really want it to reappear every 20 seconds. I just want it to pop-up and stay popped up (but not modal) until the client does something with the other browser. It's very annoying, and I have looked everywhere for an answer to this. I assume the on the fly document is the problem, how do I load my open.window after both frames have been loaded?

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