somebody found an answer here:
http://beta.experts-exchange.com/Web/Q_11543359.html
though it looks like it depends on how your javascript code is. i did a test w/ my own popup code and had your same problem in IE6.
it appears to be a 'bug' in the browser.
you may have better luck posting this in a forum for HTML, or JavaScript, or any other forum rather than a PHP help forum, as it's not a PHP question.