I had this problem a while back using v5.7: http://forum.mikrotik.com/t/ssh-between-routers-works-in-terminal-but-not-in-script/56818/1 never found an answer… but I have not tried it again on more recent versions.
MikroTik says Netwatch won’t work with private keys: http://forum.mikrotik.com/t/problem-with-ssh-client-user-option-not-working/60288/1