Comment 5 for bug 411890

https://launchpad.net/ubuntu/karmic/i386/autoconf

This page says:

"This version of autoconf is not compatible with scripts meant for
 Autoconf 2.13 or earlier. If you need support for such scripts,
 you must also install the autoconf2.13 package."

If you choose install autoconf2.13 package in addition to the 2.64, then the default autoconf executable(s) are changed to the 2.13 versions. The newest autoconf2.64 becomes a secondary, and accessible as 'autoconf2.64'. When you uninstall 2.13, then the 2.64 is put back as the primary again.

So perhaps autoconf2.13 can be added as a php5 build - time dependency. Needs testing.