When using disk encryption (e.g. ecryptfs) to protect your private home dir data, ssh pubkey authentication breaks as a side effect. It breaks for obvious reasons though. Your authorized_keys file lives in ~/.ssh/ which is intentionally encrypted when you are not logged in.
A trivial change to still allow password less/free logins, is to add a second authorized_keys file location to /etc/ssh/sshd_config. Just add/change AuthorizedKeysFile to point to '%h/.ssh/authorized_keys /etc/ssh/%u/authorized_keys'. This makes ssh first look into ~/.ssh/ and fall back to /etc/ssh/~/ if no valid authorized_keys file can be found (make sure to chown ownership of the latter to the login user).