Version:           3.1.1 (using KDE KDE 3.1.1a)
Installed from:    Debian stable Packages
Compiler:           Debian package (not sure what version)
OS:          Linux

STEPS TO REPLICATE PROBLEM
(using the script below)

1) click the link "Pop it" 
2) then click on main window
3) click "Pop it" again 

PROBLEM: the popup is not brought into focus

<script>
function poptastic(url)
 {
        var newwindow;
        newwindow=window.open(url,'popsome','height=400,width=200');
        newwindow.focus();
}
</script>
<a href="javascript:poptastic('some_url.html');">Pop it</a>