I continue this thread 'cause I have a similar issue.
I installed an additional PHP version followinf this tuto : How To Use Multiple PHP Versions (PHP-FPM & FastCGI) With ISPConfig 3 (Ubuntu 13.04)
I m on a Gentoo, but the process is the same...
I just followed the first step for PHP-FPM with PHP 5.3.24
(I had already PHP 5.4 installed and I just wanted ti use the 5.3 for a website)
unfortunately PHP is not parsed too...
I installed mod_fastcgi as written below, and here's my fastcgi.conf :
AddHandler fastcgi-script .fcgi
If someone have an idea, he's welcome ;-)
thanks per advance