OS and server information:
I previously had php 5.3.x installed but decided to upgr
I previously has a similar issue, after upgrading from 5.3 to 5.4. But my setup looks a little bit different as that I'm running Debian and using fcgid to server the PHP pages, and not the PHP5 apache/cgi module. So after I upgraded, it also installed php5_cgi, which collided with my fcgid setup, and would not execute PHP files anymore.
I had to disable the Apache Module and restart Apache
a2dismod php5_cgi
/etc/init.d/apache2 restart
Once the php5_cgi module was out of the way, fcgid was able to serve PHP pages again.