Clean URL on Drupal Multisite


I have installed drupal6.17 on a subdirectory ( NOT on Root) like,

then i created a new site applying multisite method i.e which runs normal.

Now my problem is the clean url works on but does not work with new site

the htaccess rewrite rule is used as original from drupal

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]

when i use with a slash like below, then it works with secondsite, but fails on firstsite.

RewriteRule ^(.*)$ /index.php?q=$1 [L,QSA]

Also i tried with

RewriteRule ^(.*)/$ index.php?q=$1 [L,QSA] which not working on 2nd site.

Any suggestion will be grate help!