Apache/2.2.14 (Ubuntu) - 2.3.7/silverstripe_version
In sapphire/main.php there is a comment that reads:
* It's important that requests that point directly to a file aren't rewritten; otherwise, visitors
* won't be able to download any CSS, JS, image files, or other downloads.
*
* On Apache, RewriteEngine can be used to do this.
*
* @package sapphire
* @subpackage core
* @see Director::direct()
My server is doing exactly this. If I write in my domain name with no file name (e.g. www.myDomain.com) in the address bar my site works. If I write the domain plus a file name (e.g. www.myDomain.com/index.php) then I get the home page with no CSS, or Javascript etc. Using firebug I can see the some requests are messed up (e.g. http://assets, http://jsparty, http://sapphire).
This came about because I recreated my site from an old backup after moving house and server. For some reason the original index.php was missing from all my backups except one.
I am not sure if the index.php I eventually did find is the right one for my Silverstripe version (version: 2.3.7).