Funny...

#!/usr/bin/perl

use warnings;
use strict;
use Net::FTP;

my $ftp = Net::FTP->new("ftp.cdrom.com") 
    or die "Couldn't connect: $@\n";
$ftp->login("ftp", 'warez@');
$ftp->cwd("/.2/simtelnet/gnu/djgpp/v2/");
$ftp->binary;
$ftp->pasv;
$ftp->get("faq230s.zip");
$ftp->close;
print "Th Th Tha That's All Folks!!!!!", "\n";
[download]

(file chosen at random from simtelnet at cdrom)

This works as expected, and the zip downloads fine, at least on a UNIX system. One other thing I'd try: place binmode() towards the top of the program; see how that fares. Perl may be converting your "\n" to "\r\n", which is not what you'd want.

Further, check the return of $ftp->get for the filename and check the filesizes to see if they're identical. Also, make sure the file doesn't exist first on the local side, if at all possible.