In my case I was trying to get PHP playing nicely with my FuelPHP app running on Apache under FCGId configured via Virtualmin.  My .htaccess looked like:

<IfModule mod_rewrite.c>
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule>

The fix was annoyingly simple and took me hours of digging to discover.  Insert a question mark before the slash after index.php like this:

<IfModule mod_rewrite.c>
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L]
</IfModule>

Alternatively you can also get it to work WITHOUT adding in the question mark by changing from FCGid to CGI (if configuring via Virtualmin: Server Configuration: Website Options: PHP script execution mode from “FCGId” to “CGI wrapper”) but if you want it to work in FCGid mode you will need the question mark.  I do not know why this is the case though.