In his infinite wisdom the FreeBSD PHP4 port maintainer has decided to modify the way it gets installed (again!!). After breaking nearly every website on the server for a few minutes, I found the solution here: http://www.moundalexis.com/archives/000045.php.
In short, edit the makefile in the port dir and remove the --disable-all from the configure flags. Then do the port upgrade.
That'll teach me to read the CHANGES file before upgrading.