Funny thing is, this code workes just fine if i dont go for a sub and have all the code in dl.pl BUT as soon as i move the code in a sub, the downloaded file is called after the script (ie dl.pl)

Unlikely story; did you look inside the downloaded file? Did you look in your error logs?

Content-Disposition... odd behavior in IE, Re: How to download a file from the server (content disposition CGI->header( qw{ -type mime/type -attachment filename } ) )