בעיה עם clean url

שלום,
אני מנסה להתקין אתר דורפל על שרת vps שאני מחזיק.
על השרת רצות כבר כמה אפליקציות בינהן אפליקציות java , משום כך אני משתמש בvirtual hosts.
ניסיתי כל מה שמצאתי באנטרנט על קונפיגורציה של clean url והתקנתי ואיפשרתי את המודול rewrite . מערכת ההפעלה היא ubuntu 10.04.

הנה הקבצים הרלוונטים:
cat /etc/apache2/sites-available/
default default-ssl dev1.mydomain2.com ssl www.mydomain.com www.my-domain.com www.mydomain3.com
root@0nline-estimate:~# cat /etc/apache2/sites-available/www.my-domain.com
NameVirtualHost my-ip:80

ServerAdmin webmaster@localhost
ServerAlias my-domain.com
RewriteEngine On
RewriteOptions inherit
DirectoryIndex index.html
DocumentRoot /var/www/my-domain/

if using awstats

we want specific log file for this server

CustomLog /var/log/apache2/www.my-domain.com-access.log combined

AllowOverride All

RewriteEngine on
RewriteBase /my-domain
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]

AccessFileName .htaccess

cat /var/www/my-domain/.htaccess
#

Apache/PHP/Drupal settings:

#

Protect files and directories from prying eyes.

Order allow,deny

Don't show directory listings for URLs which map to a directory.

Options -Indexes

Follow symbolic links in this directory.

Options +FollowSymLinks

Make Drupal handle any 404 errors.

ErrorDocument 404 /index.php

Force simple error message for requests for non-existent favicon.ico.

# There is no end quote below, for compatibility with Apache 1.3.
ErrorDocument 404 "The requested file favicon.ico was not found.

Set the default handler.

DirectoryIndex index.php

Override PHP settings. More in sites/default/settings.php

but the following cannot be changed at runtime.

PHP 4, Apache 1.

php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
php_value mbstring.http_input pass
php_value mbstring.http_output pass
php_value mbstring.encoding_translation 0

PHP 4, Apache 2.

php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
php_value mbstring.http_input pass
php_value mbstring.http_output pass
php_value mbstring.encoding_translation 0

PHP 5, Apache 1 and 2.

php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
php_value mbstring.http_input pass
php_value mbstring.http_output pass
php_value mbstring.encoding_translation 0

Requires mod_expires to be enabled.

# Enable expirations.
ExpiresActive On

# Cache all files for 2 weeks after access (A).
ExpiresDefault A1209600

# Do not allow PHP scripts to be cached unless they explicitly send cache
# headers themselves. Otherwise all scripts would have to overwrite the
# headers set by mod_expires if they want another caching behavior. This may
# fail if an error occurs early in the bootstrap process, and it may cause
# problems if a non-Drupal PHP file is installed in a subdirectory.
ExpiresActive Off

Various rewrite rules.

RewriteEngine on

# If your site can be accessed both with and without the 'www.' prefix, you
# can use one of the following settings to redirect users to your preferred
# URL, either WITH or WITHOUT the 'www.' prefix. Choose ONLY one option:
#
# To redirect all users to access the site WITH the 'www.' prefix,
# (http://example.com/... will be redirected to http://www.example.com/...)
# adapt and uncomment the following:
RewriteCond %{HTTP_HOST} ^my-domain.com$ [NC]
RewriteOptions inherit
# RewriteRule ^(.)$ http://www.my-domain.com/$1 [L,R=301]
#
# To redirect all users to access the site WITHOUT the 'www.' prefix,
# (http://www.example.com/... will be redirected to http://example.com/...)
# uncomment and adapt the following:
# RewriteCond %{HTTP_HOST} ^www.example.com$ [NC]
# RewriteRule ^(.)$ http://example.com/$1 [L,R=301]

# 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 /my-domain

# Rewrite URLs of the form 'x' to the form 'index.php?q=x'.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^(.*)$ /index.php?q=$1 [L,QSA]

$Id: .htaccess,v 1.90.2.5 2010/02/02 07:25:22 dries Exp $

אודה מאוד אם למישהו יש הצעה לפתרון , אני כבר מנסה כמה ימים