Follow-on from my post above (Re: Using Net::SSH2::Cisco), I tested something simple against a 7200-series router:

#!perl

use strict;
use warnings;

use Net::SSH2::Cisco;

my $host = Net::SSH2::Cisco->new(
    host => '10.254.254.1',
    dump_log => 'out.txt',
);

$host->login(
    name => 'cisco',
    password => 'cisco',
);

my @ret = $host->cmd(
    "copy running-config tftp://192.168.100.254\n\n\n"
);

print @ret;

$host->close;
[download]

... and it works fine (note my TFTPd server is 'tftpd-simple.pl' supplied with the Net::TFTPd module)...

VinsWorldcom@C:\Users\VinsWorldcom\tmp> test.pl
copy running-config tftp://192.168.100.254
Address or name of remote host [192.168.100.254]?
Destination filename [r1-confg]?
!!
9721 bytes copied in 4.400 secs (2209 bytes/sec)
[download]

I think you need to boil your script down to basics, get something that works, then starting adding the threads and other special stuff. Notice I didn't use waitfor() or change timeout() - I'm just using defaults. Note also that I tested and it works just as well when using Net::Telnet::Cisco (instead of Net::SSH2::Cisco - s/SSH2/Telnet/g) - as it should since Net::SSH2::Cisco is supposed to be a drop and replace SSH solution for the Net::Telnet::Cisco one.