I ended up trying the long timeout thing and it did work but it would allow the value(in seconds) of the timeout to pass in between commands.

For example: timeout = 5

It will take 5 seconds to login, then it will take 5 seconds for the first command to be issued, then another 5 seconds for the next command, so on so forth. and finally 5 seconds for the close command.

So, in the end, the process ends up spending way too much time per device and therefore this was a show stopper for me.

The solution for me (since Salva's solution didn't work for me in this thread Net::OpenSSH multiple commands ) was to remove the username/password login and make it use public-key authentication. So far (knock on wood) I haven't had this problem again and the delay in between the commands is gone. This seems to finally round off this solution for me. Here is a sample of code I used to make this work. (taken from it's documentation)

# Starting ssh without password
# 1) run the constructor
my $ssh = Net::SSH::Expect->new (
  host => "myserver.com", 
  user => 'bnegrao', 
  raw_pty => 1
);
# 2) now start the ssh process
$ssh->run_ssh() or die "SSH process couldn't start: $!";
        
# 3) you should be logged on now. Test if remote prompt is received:
($ssh->read_all(2) =~ />\s*\z/) or die "where's the remote prompt?"

$ssh->exec("whoami");
$ssh->exec("/sbin/ifconfig");
$ssh->exec("ls /");

ssh->close();
[download]

I know this post is old but I hope this helps someone anyway.