Ok, now I've added code tags, I can see what you're doing and can make another suggestion.

you're telling the browser that your output is HTML (in the content type header). But actually, you're not sending HTML, you're sending plain text. If you tell the browser that you're sending plain text, then it will treat your output as plain text and honour your newlines.

The simplest way to do that is to change your content type header:

print "Content-type:text/plain\n\n";
[download]

But as you're using CGI.pm, why not use the header function to make your life easier:

print header(-type => 'text/plain');
[download]