»make distclean« forgets to delete »tests/crls.d« and »tests/S.dirmngr«.
Try this:
tar jvxf gnupg-2.1.3.tar.bz2
cp -a gnupg-2.1.3 gnupg-2.1.3.original
./configure
make
make install
make distclean
diff -r gnupg-2.1.3 gnupg-2.1.3.original