sorry, I didn't explain well.
I've a project, in the setup.py file, I've a function called update_prefix, that updates the 'path_project' variable with prefix arguments from setup.py
If you runs setup.py with --prefix=/usr, then the file in 'projectname/projectnameconfig.py' is modified changing the 'path_project' variable from @PREFIX@+"share/projectname" to '/usr/share/projectname'.
If you runs setup.py without prefix arguments, the prefix is '/usr/local'.

Debuild which is the tool used to build debian package, in this case using CDBS, gives this output:
it first runs:
...
python setup.py build \
--build-base="/tmp/buildd/pdal2-0.3.1/./build"
running build
running build_py
creating /tmp/buildd/pdal2-0.3.1/build
creating /tmp/buildd/pdal2-0.3.1/build/lib.linux-i686-2.7
creating /tmp/buildd/pdal2-0.3.1/build/lib.linux-i686-2.7/pdal
copying pdal/utils.py -> /tmp/buildd/pdal2-0.3.1/./build/lib.linux-i686-2.7/pdal
copying pdal/pdalconfig.py -> /tmp/buildd/pdal2-0.3.1/./build/lib.linux-i686-2.7/pdal
...
then it runs:
...
cd . && \
		python setup.py install \
		--root="/tmp/buildd/pdal2-0.3.1/debian/pdal2/" \
		--install-purelib=/usr/lib/python2.7/site-packages/ \
		--prefix=/usr --no-compile -O0 --install-layout=deb 
running install
running build
running build_py
running build_scripts

It doesn't copy pdal/pdalconfig.py becouse the file in /tmp/buildd/pdal2-0.3.1/./build/lib.linux-i686-2.7/pdal have the same st_mtime in seconds than pdal/pdalconfig.py, but if you see de st_mtime, both are different in millisec and the file is different.

 File: «pdal/pdalconfig.py»
Modify: 2011-11-16 11:55:52.665727826 +0100

File: «/tmp/buildd/pdal2-0.3.1/./build/lib.linux-i686-2.7/pdal/pdalconfig.py»
Modify: 2011-11-16 11:55:52.000000000 +0100

but if you print the st_mtime of both files within newer() function you can check the file's timestamp are the same when they are really not:
ST_MTIME-source-target-1321440952-1321440952

That is cause of the issue, that I explain in the early comment, I fixed it rounding to two decimals instead of rounding to integer.