Bitnami/Wordpress Multisite: Redirect Loop

I've created a fresh (standard) WP install, moved it to the root and setup a Multisite with subfolders following the WP Codex to a tee. I've been trying to get this to work for several days now and urgently need some help as I have a deadline.

Subsites that I create cannot be accessed at wp-admin - this results in a redirect loop error. Themes/plugins to subsites are also broken. The MU site at root directory is completely accessible.

All links in the database (wp_options, wp_blogs etc) are the same, which is my root domain. Here is what is in my .htaccess at root:

# BEGIN WordPress

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

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [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