Hi,
I'm no expert here, but...
Are you sure there are no bugs in the _javascript_ that triggers the window, AND in the CGI/PERL scrripts that's supposed to warn you? CGI and PERL are really tricky. Just missing a semi-colon or forgetting to put a letter in lower-case could make the whole thing not work. Check your scripts carefully to make sure everything's the way it's supposed to be. If you are really desperate to get it working, re-write your whole script.
Also, you said that the pop-up window doesn't show up in your logs. Does anything show up at all? I mean, try accessing another portion of your website, and see if that shows up in your logs. Basically, try to make the pop-up show up in your logs.
Good luck!
