I just reproduced in a clean new jaunty up-to-date vm.

sudo apt-get install subversion
svn co svn://svn.gnome.org/svn/gtk+/trunk gtk+ && cd gtk+
sudo apt-get install --without-recommends build-essential libtool gtk-doc-tools 
autoconf automake1.7 libglib2.0-dev libatk1.0-dev libpango1.0-dev libcairo2-dev
# --help is to disable the configure run
./autogen --help
mkdir build && cd build
../configure --without-libtiff --without-libjasper
make

This fails with:
...
/usr/bin/ld:.libs/libgdk_pixbuf-2.0.ver:2: ignoring invalid character `\001' in 
script
/usr/bin/ld:.libs/libgdk_pixbuf-2.0.ver:2: syntax error in VERSION script
and indeed the build/ libtool as odd characters in it.  Note that the libtool 
script is fine after "configure" and is also fine if one reruns config.status.

This is regular jaunty so /bin/sh is dash and the above is run under
bash.

Bye,

-- 
$(SHELL) config.status broken
https://bugs.launchpad.net/bugs/332840
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