There are two MOTD's shown when I login to my server using SSH

The MOTD can either be printed by sshd, or by PAM. It's possible that both are doing it.

Check your /etc/ssh/sshd_config for the following:

PrintMotd yes

If that line isn't present it may be defaulting to yes (although Debian/Ubuntu change the default to no).

Check your PAM configuration in /etc/pam.d/ for the following:

session    optional     pam_motd.so

Try disabling these one at a time to see what changes.

If you are using Ubuntu, you might try to:

sudo nano /etc/ssh/sshd_config

and check to see of PrintMotd and UsePam are both set to true, that was the case for me.

Note: Following the above, you can do sudo service ssh restart and you should see just one Motd on login.