The problem is that CGI.pm uses param() to get parameters and not %in. It should work here...

use CGI qw/:all/;
use Fcntl qw(:flock);

print header;

# get the file from the input stream
$upload = param("UPLOAD");

# check if it's there, and write it to disk
if ($upload){
    open (TEXT, ">filename.txt") || die "$!";
    flock (TEXT, LOCK_EX) || die "$!";
    print"i had to find out if it works\n";
    while (<$upload>) {
        print TEXT ;
    }
    close(TEXT);
}
[download]