Have you compared httpd.conf to the master file? Maybe something isn't
getting loaded before that.
Are you using an include.conf file loaded before your main site? My
first site looks like:
NameVirtualHost 216.xx.xxx.xx
<VirtualHost 216.xx.xxx.xx>
ServerName host.domain.com
ServerAdmin admin
DocumentRoot /home/sites/home/web
RewriteEngine on
RewriteCond %{HTTP_HOST} !^216.xx.xxx.xx(:80)?$
RewriteCond %{HTTP_HOST} !^host.domain.com(:80)?$
RewriteRule ^/(.*) http://host.domain.com/$1 [L,R]
RewriteOptions inherit
AliasMatch ^/~([^/]+)(/(.*))? /home/sites/home/users/$1/web/$3
</VirtualHost>