Thanks for the bug report.  I installed this patch:

2006-06-30  Paul Eggert  <[EMAIL PROTECTED]>

        * tests/torture.at (Configuring subdirectories): Set CONFIG_SITE
        to a nonexistent file, so that we don't have to worry about
        a local site configuration that doesn't use /usr/local.
        Problem reported by Keith Marshall in
        <http://lists.gnu.org/archive/html/bug-autoconf/2006-06/msg00133.html>.

Index: tests/torture.at
===================================================================
RCS file: /cvsroot/autoconf/autoconf/tests/torture.at,v
retrieving revision 1.65
diff -p -u -r1.65 torture.at
--- tests/torture.at    23 Jun 2006 14:56:30 -0000      1.65
+++ tests/torture.at    30 Jun 2006 07:17:23 -0000
@@ -840,7 +840,7 @@ AT_CHECK([test -f inner/configure])
 
 # Running the outer configure recursively should provide the innermost
 # help strings.
-AT_CHECK([./configure --help=recursive | grep INNER], 0, [ignore])
+AT_CHECK([CONFIG_SITE=no-such-file ./configure --help=recursive | grep INNER], 
0, [ignore])
 
 # Running the outer configure should trigger the inner.
 AT_CHECK_CONFIGURE
@@ -853,7 +853,7 @@ prefix=/usr/local
 
 # The same, but from a builddir.
 AS_MKDIR_P([builddir])
-AT_CHECK([cd builddir && ../configure], 0, [ignore])
+AT_CHECK([cd builddir && CONFIG_SITE=no-such-file ../configure], 0, [ignore])
 AT_CHECK([cat builddir/inner/innermost/config], 0,
 [INNER=inner
 srcdir=../../../inner/innermost
@@ -866,7 +866,7 @@ prefix=/usr/local
 # that if the user has set config.site to have a config.cache, then
 # the two runs don't have colliding caches.
 AS_MKDIR_P([builddir2])
-AT_CHECK([cd builddir2 && ../configure --prefix /bad --prefix /good INNER=bad 
INNER=good], 0, [ignore])
+AT_CHECK([cd builddir2 && CONFIG_SITE=no-such-file ../configure --prefix /bad 
--prefix /good INNER=bad INNER=good], 0, [ignore])
 AT_CHECK([cat builddir2/inner/innermost/config], 0,
 [INNER=good
 srcdir=../../../inner/innermost


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