CSS an Images broken

Hi there,
I have seen many similar issues but non of them with a clear way to solve it.
I have a multisite installation with two sites, recently added a third one, my instalation is on /subdirectories/ Everything working perfectly fine with the second, no similar issues.

On this one once I chose the theme is taking the wrong path to the files adding the /subdirectory/ to the path.

I have checked my Htaccess but I have no idea what could be wrong, following your instructions on the other threads I have checked id my Htaccess matches the one on the Multisite configuration and it does not, but If I change it to the one chosen on the configuration NOTHING works.

This is My Htaccess now:

# Permanent URL redirect
Redirect 301 /blog/cursos-online-gratis-en-espanol-enero-2015 http://nomadadigital.org/blog/cursos-online-gratis-en-espanol-enero-2016
Redirect 301 /blog/media-kit-que-es-y-como-crear-uno/ http://nomadadigital.org/blog/media-kit-que-es-y-como-hacer-el-tuyo/

#Force non-www:
RewriteEngine on
RewriteCond %{HTTP_HOST} ^www\.nomadadigital\.org [NC]
RewriteRule ^(.*)$ http://nomadadigital.org/$1 [L,R=301]

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]
mod_gzip_on Yes

# BEGIN WPSuperCache

<IfModule mod_deflate.c>
  SetOutputFilter DEFLATE
  SetEnvIfNoCase Request_URI \
  \.(?:gif|jpe?g|png)$ no-gzip dont-vary
</IfModule>

<IfModule mod_expires.c>
  ExpiresActive on
  ExpiresByType image/jpg "access 2 month"
  ExpiresByType image/gif "access 2 month"
  ExpiresByType image/jpeg "access 2 month"
  ExpiresByType image/png "access 2 month"
  ExpiresByType text/css "access 2 month"
  ExpiresByType application/x-javascript "access plus 2 month"
  ExpiresByType text/javascript "access plus 2 month"
  ExpiresByType application/javascript "access plus 2 month"
  ExpiresByType image/x-icon "access plus 12 month"
  ExpiresByType image/icon "access plus 12 month"
  ExpiresByType application/x-ico "access plus 12 month"
  ExpiresByType application/ico "access plus 12 month"
</IfModule>
# END WPSuperCache
# BEGIN WordPress
# END WordPress

This is the one the installation wants me to use:

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).*) WordPress_05/$2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ WordPress_05/$2 [L]
RewriteRule . index.php [L]

Somehow with the first one the theme picks up SOME css code, not a single image. With the second one the theme picks nothing but the text.

The Theme is trying to get the file athttp://nomadadigital.org/academia/wp-content/plugins/goodlayers-lms/lms-style-custom.css

When it’s actually at http://nomadadigital.org/wp-content/plugins/goodlayers-lms/lms-style-custom.css

Any idea?
Thanks in advance