surely, you're assuming that the path to ls is with the relevant user. Try this one, though I haven't actually tested it, to be honest.... :)

use Net::SSH::W32Perl;
my $ssh = Net::SSH::W32Perl->new($host,debug=>1);
$ssh->login($user, $pass);
my($stdout, $stderr, $exit) = $ssh->cmd("/bin/bash /bin/ls -lrt");
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