I was having trouble with my VirtualHosts here. Some sites worked but some did not.
It was down to the sites that use some sort of framework, and by adding the following code into the VirtualHost section for the misbehaving site:
<Directory /path/to/site/folder> Options +Indexes +FollowSymLinks +ExecCGI DirectoryIndex index.php AllowOverride All Order allow,deny Allow from all </Directory>
I’m guessing it was preventing the mod_rewrite to do the re-writing.