setupext.py was indeed not reading the macosx build information from setup.cfg. 
I've put a patch here:

http://sourceforge.net/tracker/?func=detail&atid=560722&aid=2818964&group_id=80706

(patch number 2818964).

The error you're seeing is described in this technical note from Apple:

http://developer.apple.com/qa/qa2007/qa1567.html

One thing that changed between 0.98.5.3 and the current SVN version is that 
we're now using matplotlib's path cleanup code, which is in C++. Maybe the 
linker is picking up different libraries with C++? Though I haven't seen this 
error on Mac OS X 10.4 or 10.5.

--Michiel.

--- On Thu, 7/9/09, Robin <robi...@gmail.com> wrote:

> From: Robin <robi...@gmail.com>
> Subject: [Matplotlib-users] current svn fails to build on mac
> To: matplotlib-users@lists.sourceforge.net
> Date: Thursday, July 9, 2009, 6:11 AM
> Hi,
> 
> Just to let folks know the current SVN version fails to
> build on a
> mac. I built the release (0.98.5.3) successfully from
> source so I
> think my environment, dependencies etc. should be OK.
> 
> The problem seems to be building mac os x native backend:
> building 'matplotlib.backends._macosx' extension
> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp
> -mno-fused-madd
> -fno-common -dynamic -DNDEBUG -g -O3
> -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API
> -I/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/include
> -I/usr/local/include -I/usr/include -I/usr/X11R6/include
> -I.
> -I/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/include
> -Isrc -Iagg24/include -I.
> -I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5
> -c src/_macosx.m -o
> build/temp.macosx-10.3-i386-2.5/src/_macosx.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g
> -bundle
> -undefined dynamic_lookup
> build/temp.macosx-10.3-i386-2.5/src/_macosx.o
> build/temp.macosx-10.3-i386-2.5/CXX/cxx_extensions.o
> build/temp.macosx-10.3-i386-2.5/CXX/cxxextensions.o
> build/temp.macosx-10.3-i386-2.5/CXX/cxxsupport.o
> build/temp.macosx-10.3-i386-2.5/CXX/IndirectPythonInterface.o
> build/temp.macosx-10.3-i386-2.5/src/agg_py_transforms.o
> build/temp.macosx-10.3-i386-2.5/src/path_cleanup.o
> -L/usr/local/lib
> -L/usr/lib -L/usr/X11R6/lib -lstdc++ -lm -o
> build/lib.macosx-10.3-i386-2.5/matplotlib/backends/_macosx.so
> -framework Cocoa
> ld: cycle in dylib re-exports with
> /Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/lib/libGL.dylib
> collect2: ld returned 1 exit status
> error: command 'g++' failed with exit status 1
> 
> How can I disable building the mac os x backend. I copied
> setup.cfg.example to setup.cfg and have "macosx = False"
> but it
> doesn't seem to have any effect. "python setup.py config"
> still
> reports  "Mac OS X native: yes".
> 
> Thanks
> 
> Robin
> 
> PS - some minor comments about the sourceforge download
> page (I dont
> know if these can be changed):
> On the summary page ( http://sourceforge.net/projects/matplotlib/ )
> the "download now" link  which I would think should
> point to the
> latest release point to 0.91. Then when you do 'view all
> files'
> matplotlib-maintenance is the default expanded branch of
> the tree with
> latest version 0.91.4. To get the real new version you have
> to close
> this tree or scroll down to the normal matplotlib branch.
> If I didn't
> know the versions to look for beforehand I think this would
> be really
> confusing - can you make matplotlib the default instead of
> matplotlib-maintenance?
> Also I went to the Developer page to find the svn repo
> http://sourceforge.net/projects/matplotlib/develop and
> followed the
> instructions there which of course started to pull in the
> whole repo.
> When I found it taking a long time I noticed that I was
> getting
> branches etc I didnt need. I know this is covered with the
> correct
> command in the install page, but I thought it would be
> handy to change
> it here as well to avoid someone else making the mistake I
> made.
> These are very minor things and normally I wouldn't bother
> mentioning,
> but since the matplotlib website etc. seems so nice I
> figured there is
> someone who cares about this stuff - although I'm not sure
> whether its
> possible to change this stuff in sourceforge.
> 
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