Okay, I've given up on capturing stderr in traditional methods. I do, however, have another problem.

#!/usr/bin/perl
#
#
use Net::SSH::Perl;

my $host = "mynode";
my $user = "user";
my $pass = "pass";

my $ssh = Net::SSH::Perl->new($host, options => ["RhostsAuthentication
+ no"]);
$ssh->login($user, $pass);
my ( $stdout, $stderr, $exit ) = $ssh->cmd('uptime');

chomp $stdout;
print "$stdout\n";
[download]

On two specific nodes, I get "Permission denied" when the script tries to log in. However, when using the shell, ssh user@host, and entering the pass when prompted always works. Dose this mean that Net::SSH::Perl is not using password authentication, and is trying to use an rsa key? I think this is a setting in the sshd_config file, but am not sure which one to be honest. I need the apache user to do the ssh'ing, so setting up keys is a bit tricky.

Cheers.