Rebuilding autotools through maintainer-mode is _not_ good, because it usually means you forget to add dependencies, and they'll magically use the same version as used by upstream, which might not be what the user have installed at all. If you patch Makefile.am or configure.in/configure.ac you _have to_ use autotools.eclass and eautomake/eautoreconf. Exceptions are granted _only_ for system packages that would make it impossible to run autotools during stagebuilding. Please fix your package.
Found the problem and fixed myself.
