I reproduced the problem with the following commands:

cd py3k
export LANG=C
export LC_ALL=C
make distclean
./configure --with-pydebug --prefix=/home/haypo/tmp/py3ké
make

It looks like the problem is that srcdir environment variable of Makefile.pre is ".". In this case, VPATH environment variable is not set and so calculate_path() fails to retrieve the source code directory.

configure script contains a strange comment (whereas i cannot find "VPATH" in configure.in):

# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
# trailing colons and then remove the whole line if VPATH becomes empty
# (actually we leave an empty line to preserve line numbers).