Multisite wp-admin redirect loop

I have a subdirectory multisite setup, it all works fine apart from one small issue…

The sites are setup in the following structure:

http://domain.com/blogs/
http://domain.com/blogs/second/
http://domain.com/blogs/third/

You can access the admin panels if you use the following:

http://domain.com/blogs/wp-admin/
http://domain.com/blogs/second/wp-admin/index.php
http://domain.com/blogs/third/wp-admin/index.php

But if you use the following (as wordpress does in the dashboard), then it gives a redirect loop?

http://domain.com/blogs/second/wp-admin/
http://domain.com/blogs/third/wp-admin/

It seems there is some sort of redirect just when index.php is not specified on the subfolder installs, what is causing this?!

This multisite setup was setup in WordPress 3.9.1 or before.

.htaccess

# BEGIN WordPress
<IfModule mod_rewrite.c>
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]
</IfModule>
# END WordPress