This issue relates to differences between apache 2.2 and the newer 2.4.
You'll need to add this to your httpd.conf file where you set the vhost directory:
AllowOverride All
DirectoryIndex disabled
Options MultiViews Indexes SymLinksIfOwnerMatch IncludesNoExec
I found the XAMPP and other stacks running 2.4 apache work fine after that and you can leave your indoex.php where it is (even tough technically you can remove it as htaccess does all the work there).
See https://groups.google.com/forum/#!topic/silverstripe-dev/-xH6yZfC5Tc
Hope that solves it for you.