From the debug output it looks like the script is connecting using passive mode - you can see this from the line

Net::FTP=GLOB(0x9da13a0)>>> PASV
[download]

... it then times out for some reason - presumably because it is not receiving any data from ftp.cpan.org (maybe this is being firewalled out.
(more info on passive/active FTP here: http://slacksite.com/other/ftp.html)

... which is strange since when I run the same script it does not enter passive mode...

Net::FTP>>> Net::FTP(2.77)
Net::FTP>>>   Exporter(5.58)
Net::FTP>>>   Net::Cmd(2.28)
Net::FTP>>>   IO::Socket::INET(1.31)
Net::FTP>>>     IO::Socket(1.30)
Net::FTP>>>       IO::Handle(1.27)
Net::FTP=GLOB(0x22d19c)<<< 220 Welcome to the ftp.linux.hr FTP service
+.
Net::FTP=GLOB(0x22d19c)>>> USER anonymous
Net::FTP=GLOB(0x22d19c)<<< 331 Please specify the password.
Net::FTP=GLOB(0x22d19c)>>> PASS ....
Net::FTP=GLOB(0x22d19c)<<< 230-
Net::FTP=GLOB(0x22d19c)<<< 230-Ovo je ftp.linux.hr, FTP posluzitelj Hr
+vatske Udruge Linux Korisnika.
Net::FTP=GLOB(0x22d19c)<<< 230-
Net::FTP=GLOB(0x22d19c)<<< 230-Pogledajte README datoteku za opis sadr
+zaja na nasem posluzitelju.
Net::FTP=GLOB(0x22d19c)<<< 230-
Net::FTP=GLOB(0x22d19c)<<< 230-CD ISO imagei su na iso.linux.hr!
Net::FTP=GLOB(0x22d19c)<<< 230-
Net::FTP=GLOB(0x22d19c)<<< 230- -- ftpadmin@linux.hr
Net::FTP=GLOB(0x22d19c)<<< 230 Login successful.
Net::FTP=GLOB(0x22d19c)>>> CWD /pub/CPAN
Net::FTP=GLOB(0x22d19c)<<< 250-The Comprehensive Perl Archive Network 
+(http://www.cpan.org/)
Net::FTP=GLOB(0x22d19c)<<< 250-master site has been from the very begi
+nning (1995) hosted at FUNET,
Net::FTP=GLOB(0x22d19c)<<< 250-the Finnish University NETwork.
Net::FTP=GLOB(0x22d19c)<<< 250-
Net::FTP=GLOB(0x22d19c)<<< 250-
Net::FTP=GLOB(0x22d19c)<<< 250 Directory successfully changed.
Net::FTP=GLOB(0x22d19c)>>> PORT 164,48,254,74,158,171
Net::FTP=GLOB(0x22d19c)<<< 200 PORT command successful. Consider using
+ PASV.
Net::FTP=GLOB(0x22d19c)>>> RETR README.html
Net::FTP=GLOB(0x22d19c)<<< 150 Opening BINARY mode data connection for
+ README.html (5804 bytes).
Net::FTP=GLOB(0x22d19c)<<< 226 File send OK.
[download]

Maybe you can try active mode and see if that works. You can do this using the following line:

my $ftp=Net::FTP->new("ftp.cpan.org", Debug => 1, Passive => 0)
[download]

Hope that helps.