After a multiple-days debugging orgy I finally found what's triggering this. Please see https://bugzilla.gnome.org/show_bug.cgi?id=669157 for the whole story, but copying the last comment here for convenience:

The Debian package runs this snippet between configure and make, to configure static (builtin) vs. dynamic (extensions) modules:

        egrep \
          "^#($$(awk -v ORS='|' '$$2 ~ /^extension$$/ {print $$1}'
debian/PVER-minimal.README.Debian.in)XX)" \
          Modules/Setup.dist \
            | sed -e 's/^#//' -e 's/-Wl,-Bdynamic//;s/-Wl,-Bstatic//' \
            >> $(1)/Modules/Setup.local

When I disable this part, the local build works.

That code results in this Modules/Setup.local:

----------------- 8< ---------------------
# Edit this file for local setup changes
array arraymodule.c     # array objects
math mathmodule.c _math.c # -lm # math library functions, e.g. sin()
_struct _struct.c       # binary structure packing/unpacking
time timemodule.c _time.c # -lm # time operations and variables
_random _randommodule.c # Random number generator
atexit atexitmodule.c      # Register functions to be run at
interpreter-shutdown
_elementtree -DUSE_PYEXPAT_CAPI _elementtree.c  # elementtree accelerator
_pickle _pickle.c       # pickle accelerator
_datetime _datetimemodule.c     # datetime accelerator
_bisect _bisectmodule.c # Bisection algorithms
_heapq _heapqmodule.c   # Heap queue algorithm
unicodedata unicodedata.c    # static Unicode character database
fcntl fcntlmodule.c     # fcntl(2) and ioctl(2)
spwd spwdmodule.c               # spwd(3) 
grp grpmodule.c         # grp(3)
select selectmodule.c   # select(2); not on ancient System V
_socket socketmodule.c
_ssl _ssl.c -lssl -lcrypto
_posixsubprocess _posixsubprocess.c  # POSIX subprocess module helper
_hashlib _hashopenssl.c -lssl -lcrypto
syslog syslogmodule.c           # syslog daemon interface
binascii binascii.c
_ctypes _ctypes/_ctypes.c _ctypes/callbacks.c _ctypes/callproc.c
_ctypes/stgdict.c _ctypes/cfield.c _ctypes/malloc_closure.c  -lffi
zlib zlibmodule.c -I$(prefix)/include -L$(exec_prefix)/lib -lz
pyexpat pyexpat.c -lexpat
----------------- 8< ---------------------

Bisecting this quickly leads to the _ctypes module configuration.

So a small reproducer based on the upstream Python 3.2 build is:

 * Configure and build pygobject with PYTHON=python3.2  (or specify the full
path for a local python build)

 * Build python 3.2 with the broken _ctypes module configuration:

$ cd /tmp/
$ tar xf python3.2_3.2.3.orig.tar.gz
$ cd python3.2-3.2.3
$ ./configure --with-wide-unicode    # to be compatible with the Debian/Ubuntu
python 3.2
$ echo '_ctypes _ctypes/_ctypes.c _ctypes/callbacks.c _ctypes/callproc.c
_ctypes/stgdict.c _ctypes/cfield.c _ctypes/malloc_closure.c  -lffi' >>
Modules/Setup.local
$ make -j4

Then in the pygobject built tree, run

$ (cd tests; TEST_NAMES=test_everything.TestCallbacks PYTHONPATH=..:.
LD_LIBRARY_PATH=./.libs GI_TYPELIB_PATH=.  /tmp/python3.2-3.2.3/python
./runtests.py)

which reproduces the failure.

Conversely, if I change the ctypes line in debian/PVER-minimal.README.Debian.in from

  _ctypes               extension

to

  _ctypes               builtin

and build/install the packages, everything works.

For a more convenient reproducer on the Debian/Ubuntu side, you can just run "python3 set_cell_data_func.py", i. e. the attached sample code here.

So there is something wrong with how this configures the _ctypes module to be linked into python itself, instead of being a separate module (/usr/lib/python3.2/lib-dynload/_ctypes.cpython-32mu.so) that you get with "builtin" (that is indeed pretty confusing, given that I switched it _from_ "extension" _to_ "builtin". Or there is a Python 3.2/libffi bug which causes that.