Comment 2 for bug 144498

Adam has pointed out the cause of this.

22:45:04 < infinity> mdke: A quick look at the build log would lead me to believe that some sort of configure script is
                     running in the "clean" target, rather than the "build" target. Since dpkg-buildpackage runs "clean"
                     before "build", it works, but autopkgtest doesn't do so (so is stuck with the configured variables from
                     the "clean" run right before the source package was built).
22:46:52 < infinity> mdke: A look at a launchpad build log confirms that; configure is being run in "clean", not in "build".