I could not try Neal's patch since it does not seem to apply to the 
3.0a1 source I have.  But the Modules/_fileio.c patch works just fine on 
my Linux and MacOS X.  Here is the Linux result: 

$ env  LD_PRELOAD=./dlibtest4.so  ~/Python-3dbg/python
*** ctor called in python ...
*** atexit OK in python ...
Python 3.0a1 (py3k, Oct 28 2007, 10:23:59) 
[GCC 3.4.6 20060404 (Red Hat 3.4.6-8)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 
[36000 refs]
[21985 refs]
*** dtor called in python ...
$

Most interesting is that this Python build --with-pydebug now prints 2 
lines in [..] brackets on exit.  That 2nd line, [21985 refs] never 
showed up before!

Also, attached is another version of my test case renamed to dlibtest4.  
It includes 4 different use cases.  More details inside.