Multisite *mostly* working, some URLs not rendering correctly

I have multisite enabled and followed wordpress.org’s official guide to do so (don’t currently have the link). Everything seems to work pretty well except one pretty challenging issue. My primary site is called “watermint” and I have created a second site called “battleschool”. In the WordPress admin area when I hover over “My Sites” I get a dropdown showing the following options: “Network Admin”, “watermint” and “battleschool”. If I hover over battleschool and then hover over “Dashboard” the URL shown in the browser at the bottom is just http://www.mydomain.com/wp-admin, however the correct URL for navigating to the battleschool dashboard is http://www.mydomain.com/battleschool/wp-admin.

If I click the link I am taken to the default dashboard (watermint) and not battleschool. If I instead manually type in “www.mydomain.com/battleschool/wp-admin” the battleschool dashboard comes up fine. Once I am at “www.mydomain.com/battleschool/wp-admin” most things seem to work perfectly. Any of the left-hand menu options all come up with the URL containing “battleschool” but there are a couple of areas where “battleschool” is still left out of the URL (for instance the “Activate” button when activating a theme).

The problem just seems to be that although wordpress recognizes I have multiple sites, and although if I use the correct URL I am redirected correctly (.htaccess is working). There are a few places where when WP renders out links it’s not rendering them out correctly. Can someone shed some light on what’s happening?

Here’s my wp-config and just for fun my .htaccess as well.

define( 'WP_ALLOW_MULTISITE', true );
define('MULTISITE', true);
define('SUBDOMAIN_INSTALL', false);
define('DOMAIN_CURRENT_SITE', 'www.mydomain.com');
define('PATH_CURRENT_SITE', '/');
define('SITE_ID_CURRENT_SITE', 1);
define('BLOG_ID_CURRENT_SITE', 1);

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]