Clean URLS for addon domain

I've searched, to see if anybody else got a solution to the problem I'm about to describe, but I found nothing that worked for me....maybe I missed something.. if so please direct me to somewhere i can find help.

I have a siteground account with a primary domain(i.e. primary.com). Drupal works fine and clean urls is implemented.

On the account I have an addon domain which has its files stored in a subdirectory of the primary domain. The site can be reached (addon domain = example.com) at example.com , example.primary.com, and primary.com/example

I successfully installed drupal on the add on domain and have the site running, BUT when I try to run the clean url test it sends me to the home/index page.

to try to correct the problem I changed the .htaccess file
from

  # Modify the RewriteBase if you are using Drupal in a subdirectory and
  # the rewrite rules are not working properly.
  #RewriteBase /drupal

to

  # Modify the RewriteBase if you are using Drupal in a subdirectory and
  # the rewrite rules are not working properly.
  RewriteBase /example

Nothing happened when I did that after running the clean url test it still sent me to the home page.

then I changed it to

  # Modify the RewriteBase if you are using Drupal in a subdirectory and
  # the rewrite rules are not working properly.
  RewriteBase /

and again the clean url test yielded the same result.

to make sure the .htaccess was being read i tried

# Modify the RewriteBase if you are using Drupal in a subdirectory and
  # the rewrite rules are not working properly.
  RewriteBase /randomtext

and i got the same result (clean url test sends me to index) , so I thought maybe the .htaccess file changes were being saved so i deleted one of the comment tags that was needed and it produced the expected internal 500 error.

Any suggestions on how to get clean urls working???