Drupal URL Rewriting conflict
Copy from the question. I landed here wanting to help somebody and, after reading the question, I saw the solution inside...
The solution is, immediately after the RewriteEngine on rule in Drupal's .htaccess, inserting
RewriteCond $1 !^(index\.php|images|robots\.txt)RewriteRule ^ci_site/(.*)$ ci_site/index.php/$1 [L]