Media permalinks not working on subdomain sites after server move

I use my own servers. I am trying to move to a new server that is using Clearos Community 6.4 from a Windows 2003 server with IIS6. Everything works fine from moving from one server to the other, except the media permalinks. I get broken links on the subdomain sites not the main site. The media files upload correctly. I edited the line in the httpd.conf file:

<Directory />
    Options FollowSymLinks
    AllowOverride All
</Directory>

This is my .htaccess file

BEGIN WordPress
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# uploaded files
RewriteRule ^files/(.+) wp-includes/ms-files.php?file=$1 [L]

# add a trailing slash to /wp-admin
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^(.*\.php)$ $1 [L]
RewriteRule . index.php [L]
# END WordPress
# BEGIN s2Member GZIP exclusions
<IfModule mod_rewrite.c>
	RewriteEngine On
	RewriteBase /
	RewriteCond %{QUERY_STRING} (^|\?|&)s2member_file_download\=.+ [OR]
	RewriteCond %{QUERY_STRING} (^|\?|&)no-gzip\=1
	RewriteRule .* - [E=no-gzip:1]
</IfModule>
# END s2Member GZIP exclusions

Any more ideas!