Drupal clean URLs not working from subdirectory
Problem in drupal Clean URL, To Enable drupal clean url in subdirectory un comment the following line in .htaccess file.

  # Modify the RewriteBase if you are using Drupal in a subdirectory or in a
  # VirtualDocumentRoot and the rewrite rules are not working properly.
  # For example if your site is at http://example.com/drupal uncomment and
  # modify the following line:
  # RewriteBase /drupal
  #
  # If your site is running in a VirtualDocumentRoot at http://example.com/,
  # uncomment the following line:
  RewriteBase /


for more refer the blog Enable drupal clean url in subdirectory or subdomain