The aclocal.m4 as supplied didn't write files to the right places.
The etc dir was misreferenced from the lisp dir, and the code to
locate the lisp dir checked for a directory that wouldn't necessarily
exist.  I fixed the etc dir definition and changed the lisp dir code
to check for a directory that should exist. 

I also replaced the ()'s with {}'s to explicitly define the variables
at configure-time as opposed to having their definitions be based on
other variables in the Makefile.  This change made it a lot easier to
debug this particular problem so I figured it'd be useful enough to
include. 

There's one thing I'm not completely sure on -- the break line.  I
couldn't figure out why it was there.  It worked when I removed it and
it didn't work when I left it in, so I removed it.

Here's the diff:

Index: aclocal.m4
===================================================================
RCS file: /usr/local/cvsroot/gnus/aclocal.m4,v
retrieving revision 6.6
diff -r6.6 aclocal.m4
87c87
<         lispdir="\$(datadir)/${EMACS_FLAVOR}/site-packages/lisp/gnus"
---
>         lispdir="${datadir}/${EMACS_FLAVOR}/site-packages/lisp/gnus"
89c89
<     lispdir="\$(datadir)/${EMACS_FLAVOR}/site-lisp"
---
>         lispdir="${datadir}/${EMACS_FLAVOR}/site-lisp"
92,93c92
< 	potential=
< 	if test -d ${theprefix}/${thedir}/${EMACS_FLAVOR}/site-lisp; then
---
> 	if test -d ${theprefix}/${thedir}/${EMACS_FLAVOR}; then
95c94
< 	       lispdir="\$(prefix)/${thedir}/${EMACS_FLAVOR}/site-packages/lisp/gnus"
---
> 	       lispdir="${theprefix}/${thedir}/${EMACS_FLAVOR}/site-packages/lisp/gnus"
97c96
<                lispdir="\$(datadir)/${EMACS_FLAVOR}/site-lisp"
---
>                lispdir="${theprefix}/${thedir}/${EMACS_FLAVOR}/site-lisp"
99d97
< 	   break
113c111
<       etcdir="\$(lispdir)/../etc/gnus"
---
>       etcdir="\$(lispdir)/../../etc/gnus"

Jack.
-- 
Jack Twilley
jmt at twilley dot org
http colon slash slash www dot twilley dot org slash tilde jmt slash