Just to get the obvious out of the way: the commands you're issuing are working when you log in manually as the same user?

Either way I have a hunch it's unlikely that Perl's the culprit here; it's more likely it's down to environment settings of some sort. Perhaps try giving yourself an interactive shell ($ssh->shell; see the Net::SSH::Perl documentation) instead and investigate what's different there compared to a "direct" login using ssh(1).