FreeBSD pkgng vs custom ports

My Web server runs FreeBSD. Some security updates prompted me to upgrade my installed packages. Running this server entirely with packages isn’t possible, so I installed PHP 5 from ports. This machine uses pkgng.

When I ran pkg upgrade, however, my web site stopped working. The server itself started just fine, and it did quite well serving downloadable PHP code to clients. The problem was pretty obvious:

I originally compiled PHP 5 from ports so to get the Apache PHP module. Running pkg upgrade...