First do a troubleshooting test with the SSH connection as described here:
http://doc.freenas.org/11/storage.html#troubleshooting-replication#
If a password is requested, follow these steps:
http://doc.freenas.org/11/storage.html#zfs-copy-replication-key-fig
After upgrading FreeNAS it might be possible, that there is no public key assigned to the root user which prevents Replication Tasks from working. The above step should fix that.