If you are using GitHub for Windows with non-GitHub repositories, you may have run into the limitation that you cannot sync using an SSH key with a passphrase. One workaround is to push/pull from the shell, but if don’t mind removing the passphrase from the key, use the following command.

ssh-keygen -p -P "my_old_password" -N “” -f my_key_file_name

After you remove the passphrase you should be able to sync from within the GitHub for Windows client.