How about this (untested) patch to Automake?
2007-06-22 Paul Eggert <[EMAIL PROTECTED]>
* tests/subst.test: Port to CVS autoconf.
Problem reported by Benoit Sigoure in:
http://lists.gnu.org/archive/html/automake-patches/2007-06/msg00003.html
--- automake/tests/subst.test.~1.5.~ 2005-05-14 13:28:56.000000000 -0700
+++ automake/tests/subst.test 2007-06-22 14:34:32.000000000 -0700
@@ -1,5 +1,5 @@
#! /bin/sh
-# Copyright (C) 1996, 2001, 2002 Free Software Foundation, Inc.
+# Copyright (C) 1996, 2001, 2002, 2007 Free Software Foundation, Inc.
#
# This file is part of GNU Automake.
#
@@ -30,7 +30,9 @@ END
: > Makefile.am
-$ACLOCAL || exit 1
-$AUTOMAKE || exit 1
-grep '^\$1' Makefile.in && exit 1
+if $ACLOCAL; then
+ $AUTOMAKE || exit 1
+ grep '^\$1' Makefile.in && exit 1
+fi
+
exit 0
