You need to send back the HTTP header before sending any HTML. You may be doing this but it isn't happening for the code path that prints the secondary pages. Specifically, you need to set Content-Type header to text/html. Otherwise, Apache sets the default to text/plain which is what is showing up on your link above. The easiest way to do this is with the CGI.pm module's header method.

use CGI;
print header;
[download]

IE is broken and recognizes the document is HTML and displays it as a web page. Mozilla is behaving properly and shows the HTML as plaintext like the server told it to.