Thanks very much salva, your advice was brilliant. Got it working now, you've saved me days of frustration! For anyone else in my situation who is new to this stuff, I fixed this by adding the ctl_dir option:  my $ssh = Net::OpenSSH->new($host, user=>$user, ctl_dir=>$ctldir);. I created the $ctldir (called .libnet-openssh-perl) within my /var/www directory and ensured the owner was www-data.
I hope this can help someone else too! Thanks again salva, legend!