subdomain files being placed in root domain only

Hello,

I have had multisite up for a while with no issues but something has gone awry.

Not sure what went wrong but all files from different sub-domain are being directed to the primary domains “file” folder.

i.e.
original file path for domain 18 was:
domain18.com/files/imageFile.jpg
(wp-conent/blogs.dir/18/files/imageFile.jpg)

now, weird file path for domain 18 is:
mainDomain.com/files/imageFile.jpg
(mainDomain.com/files/imageFile.jpg)

Looking at the hta access file shows:

AddHandler php-stable .php

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

#Thesis Specific
RewriteRule wp-content/thesis/skins/(.*)/css.css wp-admin/admin-post.php?action=thesis_do_css

# uploaded files
RewriteRule ^files/(.+) wp-includes/ms-files.php?file=$1 [L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule . index.php [L]
# END WordPress

Looking at upload path from within Network admin at : Network Admin > Edit Site > Settings for domain 18 shows: wp-content/blogs.dir/18/files

Visually, here is what I am seeing: https://goo.gl/mv8YGs

Please help. Thanks.