Before starting, i should say I don't have this issue with Apache, only with Nginx. I'm using perusio config for Drupal 7.
I'm using the module subfolders domains (https://www.drupal.org/project/subfolders_domain) to create domains as subfolders(uri) of my main domain.
PS: This module is using the module Domain Access
This module creates symbolic links in drupal document root for each subfolder.
Example: in my Drupal document root I have several symlinks:
france -> /var/www/drupal
uk -> /var/www/drupal
index,php
modules
themes
sites...
If I browse to http://maindomain.com/france I should see the content of my subfolder france, but instead I see a 404 error.
I tried the setting disable_symlink
http://nginx.org/en/docs/http/ngx_http_core_module.html#disable_symlinks
But still no luck.
EDIT:
I have the feeling that nginx is not following the symlink before sending the url to Drupal. So Drupal is receiving this "/index.php?q=france" instead of just "/index.php".
I tried to create a symlink to an image in drupal root:
tree.png -> misc/tree.png
I have no problem to see this image in my browser.
So the problem seems to be only with symlinks and PHP.

Comments
any luck
Any luck with having subfolders_domain work with nginx?