wordpress 4.5 custom login script producing cookie error after upgrade

I have a login script that automatically logs a user in to the wordpress multisite install. using this method:

wp_set_current_user(1, "username");
wp_set_auth_cookie(1, true);
do_action('wp_login', "username");

after I updated to 4.5 from 4 I am getting an issue where the user is not logged in. I am getting no error from the code so I looked at the cookies that are being generated.

What I noticed was that the cookies that wordpress created for the login are missing the token in the name.

i.e cookie name is wordpress_logged_in_ instead of wordpress_logged_in_1dd899d5b4da8f8277be2998fcc7d357

the content of the cookie appears correct and the domain and expire time are correct.

I have looked at the function wp_set_auth_cookie and in 4.5 token was added to the function but it is optional.
https://developer.wordpress.org/reference/functions/wp_set_auth_cookie/#source-code

I would grateful for some help with this.

Thanks