Links to start of mentioned threads on autoconf and automake mailing lists.
http://lists.gnu.org/archive/html/autoconf/2008-07/msg00065.html
http://lists.gnu.org/archive/html/automake/2008-07/msg00089.html

Tor, your "Linux 2.6 x86-64 gcc 4.2.1" autobuilds have nearly the same
tools versions than the Solaris one with the exception of automake
1.10 instead of 1.10.1 and GNU m4 version 1.4.10 instead of 1.4.5

If you could temporally downgrade GNU m4 1.4.10 down to 1.4.5 on the
box running "Linux 2.6 x86-64 gcc 4.2.1" autobuild, this would give a
theoretical similar scenario, that would at least give us a little bit
more info to further pinpoint if that set of tool versions is the
problem or if the problem only triggers on Solaris.

Another idea Tor. Download m4 1.4.5 source code from
ftp://ftp.gnu.org/gnu/m4/m4-1.4.5.tar.gz and build and test it for
yourself.

I downloaded, built and run its tests:

cd m4-1.4.5
./configure
make
make check

[...]
Skipped checks were:
  ./056.changeword ./057.changeword ./058.changeword ./059.changeword
Failed checks were:
  ./079.regexp:out
make[1]: *** [check] Error 1
make[1]: Leaving directory `/home/yang/m4-1.4.5/checks'
make: *** [check-recursive] Error 1

I ignored the failed test and renamed my old m4 version out of the way
and copied the 1.4.5 in place, and afterwards tried to run buildconf.
Surprise surprise.

$ ./buildconf
buildconf: autoconf version 2.61 (ok)
buildconf: autom4te version 2.61
buildconf: autoheader version 2.61 (ok)
buildconf: automake version 1.10.1 (ok)
buildconf: aclocal version 1.10.1
buildconf: libtool version 1.5.27 (ok)
buildconf: libtoolize found
buildconf: GNU m4 version 1.4.5 (ok)
buildconf: running libtoolize
buildconf: running aclocal
/usr/bin/m4: unrecognized option `--debugfile=autom4te.cache/traces.0t'
Try `/usr/bin/m4 --help' for more information.
autom4te-2.61: /usr/bin/m4 failed with exit status: 1
aclocal-1.10: autom4te failed with exit status: 1
The aclocal command line failed

autom4te from autoconf 2.61 emmits a command line option that the
standard GNU m4 1.4.5 does not have "--debugfile".

I edit autom4te and find 2 times "--debugfile" one inside a comment
which I leave alone and another one which I replace with
"--error-output", saving changes.

New try to run buildconf... This time it succeeds.

As a test. If you build your own GNU m4 1.4.5 and try to use it you
will know if the problem is actually the blastware distributed binary
or not.

-- 
-=[Yang]=-