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://ift.tt/1Cu9fw2
http://ift.tt/1JUWoU2
http://ift.tt/1Cu9g2Q

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

http://ift.tt/1JUWnzq
http://ift.tt/1JUWoU6
http://ift.tt/1Cu9g2U

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

http://ift.tt/1JUWnzs
http://ift.tt/1Cu9g2W

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