Multisite subfolder admin urls incorrect

I have a fresh install of WordPress 4.0 and before installing any themes or plugins I enabled multisite following the instructions on the WordPress website.

I added the following to wp-config.php

/* Multisite */
define('MULTISITE', true);
define('SUBDOMAIN_INSTALL', false);
define('DOMAIN_CURRENT_SITE', 'domain.com');
define('PATH_CURRENT_SITE', '/');
define('SITE_ID_CURRENT_SITE', 1);
define('BLOG_ID_CURRENT_SITE', 1);

And my .htaccess file is as follows:

# BEGIN WordPress
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]
# END WordPress

When I log in and try to go to any of the “My Sites” links on the admin bar, all links point to my main install’s wp-admin/ instead of the subfolder site’s wp-admin/ (ie. point to domain.com/wp-admin/ instead of domain.com/site2/wp-admin/). Furthermore, when I try to active a theme it activates it on my main site instead of the subfolder site. The admin URLs seem to be leaving off the subfolder completely in all areas of the second site admin.

If I edit the site in Network Admin
Domain for the second site is : https://domain.com
Path for second site is: /site2/