Hi @Pakhil. Yes, this seems like a likely cause for the problem. You're using version 0.4.1-1 which is quite a bit older than the current release (0.10.1). I believe you can follow these instructions to use the Certbot auto installer to install the latest version.
@bmw, @erica, @schoen Do you know a better way to upgrade from 0.4.1-1 without losing state on 16.04? Am I correct in assuming that the deserialization error @pakhil is experiencing is from the old certbot?