What you were using before was most probably gnome-keyring/seahorse, which is automatically starting with the system, loading your keys and offering them to the ssh.
Regardless agent/keyring, it should start before your graphical session so all the other terminals and apps will see the authentication socket for the agent. This is usually set up in the ....
Try bookmarking the root folder on the server (Use the folder context menu). Close the connection and click on the bookmark. When asked for your password select "Keep for ever". Note: You can rename the bookmark to whatever is most helpful for you. Unfortunately, at the moment, you cannot move outside of the "Personal bookmarks" section.
It actually works if you use the default id file (~/.ssh/id_rsa). You need to enter the server name like user@host and leave user name and password fields blank. Then, there comes a pop-up asking you to enter the id file password and all works.
Make sure you got the right connection information. This is not a system error.
More information about SSH and how to use it: https://wiki.archlinux.org/index.php/Secure_Shell#Client_usage
(ArchLinux wiki. Excellent documentation)
If you need to add a PublicKey to connect (As the error message suggest) and you're unaware of it, you should try contacting ...
If the message messes the protocol, it is not MotD nor Banner, but it is written from some of the startup scripts. You should check for ~/.bashrc or other scripts used by your shell.
Consult your shell manual page to see what scripts are being used at startup, grep over the /etc/ where this string is written.
The warning is about the permissions of your private ssh key on your local host (~/.ssh/id_rsa) and you might want to try to reset the permissions to their defaults with
chmod 700 ~/.ssh/
chmod 600 ~/.ssh/id_rsa