The "Referer" is something you can NEVER rely on. It's completely up to the user-agent whether it is sent at all and what's in it. Even if the referer was your script1.cgi would not mean that the user has ever triggered that URL, it might be, the user might also trick you. IE seems to treat Javascript-redirects as something without referer, that's up to him and OK, just as it is OK when Mozilla thinks otherwise.

If you want to make sure your second script is run, you must not rely on the client: Javascript is not supported by all browsers and not actived by all users, HTML-redirects (http-equiv="refresh") may be ignored, as well as a Staus 301/302/303 HTTP-Redirect. You must solve the problem within the server. Maybe by using exec, or do, or require, or by turning script2.cgi into a Perl Module and use that module from script1.cgi ...