How to debug autoconf issues?

[m h]

Hi folks-

First of all thanks for your work on this very important piece of
software.  You probably just hear gripes and bug reports (here's
another ;)), so I want to say thanks for your efforts.  They are very
commendable.

I'm working with a few of the alt-gentoo developers who are trying to
get portage (the gentoo linux build framework) to work on non-gentoo
systems.  The idea being you install portage in a "prefixed"
environment.  This environment is sort of a sandboxed filesystem. 
(Fink and openpkg are existing examples of this).  Then the user can
install whatever software portage supports easily into the sandboxed
environment.

I'm running into configure issues that I can't seem to resolve.  (I
wouldn't call myself a C programmer.  I'm much more comfy in python. 
But I can get around a linux system).  My issue is that when portage
runs the "./configure" I get errors like the following:
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files...
checking whether we are using the GNU C compiler... no
checking whether i686-pc-linux-gnu-gcc accepts -g... no
checking for i686-pc-linux-gnu-gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E
checking for a BSD-compatible install... /data1/portage/jan6/prefix/toolsbox-4-p
atchespre.20060106/i686-pc-linux-gnu//bin/ginstall -c
checking whether make sets $(MAKE)... no
checking for ed... ed
checking for egrep... grep -E
checking for AIX... no
checking for ANSI C header files... no
checking for sys/types.h... no
checking for sys/stat.h... no
checking for stdlib.h... no
checking for string.h... no
checking for memory.h... no
checking for strings.h... no
checking for inttypes.h... no
checking for stdint.h... no
<snipped....>
checking stddef.h presence... yes
configure: WARNING: stddef.h: present but cannot be compiled
configure: WARNING: stddef.h: check for missing prerequisite headers?
configure: WARNING: stddef.h: proceeding with the preprocessor's result
configure: WARNING:     ## ------------------------------------ ##
configure: WARNING:     ## Report this to address@hidden ##
configure: WARNING:     ## ------------------------------------ ##
checking for stddef.h... yes
checking wchar.h usability... no
checking wchar.h presence... yes
configure: WARNING: wchar.h: present but cannot be compiled
configure: WARNING: wchar.h: check for missing prerequisite headers?
configure: WARNING: wchar.h: proceeding with the preprocessor's result
configure: WARNING:     ## ------------------------------------ ##
configure: WARNING:     ## Report this to address@hidden ##
configure: WARNING:     ## ------------------------------------ ##
checking for wchar.h... yes
<snipped....>

Disconcerting is the mention that there is no GNU C compiler (which is
sitting in $PREFIX/bin/gcc) and the "WARNING"s.
When the same configure command from the command line (using the same
env variables, since PATH is adjusted for the prefixed environment),
it works.
I've tried diffing the output of "env" (redirected it to a file in
portage) and can't find a difference.
I'm sure I'm missing something, but like I said I'm not really a C
developer, so I thought I'd ask here for some advice.  (Plus it said I
should report the "bug", so I guess I'm just doing my job;)  Though I
think the bug is with something I'm doing).  How do you guys debug
issues like this?  Any tips or tricks would be greatly appreciated.

thanks again,

matt