Here are the answers to your questions.

% python
Python 2.6.2 (r262:71600, Apr 16 2009, 09:17:39) 
[GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> f = open('Lib/distutils/command/wininst-6.0.exe')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
IOError: [Errno 21] Is a directory: 'Lib/distutils/command/wininst-6.0.exe'

>>> import os
>>> os.path.isdir('Lib/distutils/command/wininst-6.0.exe')
True

>>> os.stat('Lib/distutils/command/wininst-6.0.exe')
posix.stat_result(st_mode=16877, st_ino=6314085L, st_dev=234881026L, st_nlink=2, st_uid=501, 
st_gid=501, st_size=68L, st_atime=1242244664, st_mtime=1241712622, st_ctime=1241712622)

>>> os.stat('Lib/distutils/command')
posix.stat_result(st_mode=16877, st_ino=6314060L, st_dev=234881026L, st_nlink=58, st_uid=501, 
st_gid=501, st_size=1972L, st_atime=1242244781, st_mtime=1242245012, st_ctime=1242245012)


But here is the root cause.  The Python-3.1b1 files were created by Stuffit Expander ffrom the original 
Python-3.1b1 tar ball downloaded from the Python website.  Changing the Stuffit preferences does not 
make any difference.  

However, if that same tar ball is uncompressed by the  tar -zxf ... command, there are no directories.  
Only five simple files, as expected:

-rw-r--r--   1 jean  jean   61440 Jul 15  2008 wininst-6.0.exe
-rw-r--r--   1 jean  jean   65536 Jul 15  2008 wininst-7.1.exe
-rw-r--r--   1 jean  jean   61440 Jan 20 13:25 wininst-8.0.exe
-rw-r--r--   1 jean  jean  224256 Jan 29 05:08 wininst-9.0-amd64.exe
-rw-r--r--   1 jean  jean  196096 Jan 29 05:08 wininst-9.0.exe


After removing the directory files (and renaming the *.1.exe to *.exe), the regression tests passes.

% ./python.exe ../Python-3.1b1/Lib/test/test_distutils.py
test_formats (distutils.tests.test_bdist.BuildTestCase) ... ok
test_simple_built (distutils.tests.test_bdist_dumb.BuildDumbTestCase) ... ok
test_no_optimize_flag (distutils.tests.test_bdist_rpm.BuildRpmTestCase) ... ok
test_quiet (distutils.tests.test_bdist_rpm.BuildRpmTestCase) ... ok
test_get_exe_bytes (distutils.tests.test_bdist_wininst.BuildWinInstTestCase) ... ok
test_build_libraries (distutils.tests.test_build_clib.BuildCLibTestCase) ... ok
test_check_library_dist (distutils.tests.test_build_clib.BuildCLibTestCase) ... ok
test_finalize_options (distutils.tests.test_build_clib.BuildCLibTestCase) ... ok
test_get_source_files (distutils.tests.test_build_clib.BuildCLibTestCase) ... ok
test_build_ext (distutils.tests.test_build_ext.BuildExtTestCase) ... ok
test_optional_extension (distutils.tests.test_build_ext.BuildExtTestCase) ... ok
test_solaris_enable_shared (distutils.tests.test_build_ext.BuildExtTestCase) ... ok
test_user_site (distutils.tests.test_build_ext.BuildExtTestCase) ... ok
test_empty_package_dir (distutils.tests.test_build_py.BuildPyTestCase) ... ok
test_package_data (distutils.tests.test_build_py.BuildPyTestCase) ... ok
test_build (distutils.tests.test_build_scripts.BuildScriptsTestCase) ... ok
test_default_settings (distutils.tests.test_build_scripts.BuildScriptsTestCase) ... ok
test_version_int (distutils.tests.test_build_scripts.BuildScriptsTestCase) ... ok
test_check_all (distutils.tests.test_check.CheckTestCase) ... ok
test_check_document (distutils.tests.test_check.CheckTestCase) ... ok
test_check_metadata (distutils.tests.test_check.CheckTestCase) ... ok
test_check_restructuredtext (distutils.tests.test_check.CheckTestCase) ... ok
test_simple_run (distutils.tests.test_clean.cleanTestCase) ... ok
test_dump_options (distutils.tests.test_cmd.CommandTestCase) ... ok
test_ensure_dirname (distutils.tests.test_cmd.CommandTestCase) ... ok
test_ensure_filename (distutils.tests.test_cmd.CommandTestCase) ... ok
test_ensure_string (distutils.tests.test_cmd.CommandTestCase) ... ok
test_ensure_string_list (distutils.tests.test_cmd.CommandTestCase) ... ok
test_make_file (distutils.tests.test_cmd.CommandTestCase) ... ok
test_server_empty_registration (distutils.tests.test_config.PyPIRCCommandTestCase) ... ok
test_server_registration (distutils.tests.test_config.PyPIRCCommandTestCase) ... ok
test_clean (distutils.tests.test_config_cmd.ConfigTestCase) ... ok
test_dump_file (distutils.tests.test_config_cmd.ConfigTestCase) ... ok
test_finalize_options (distutils.tests.test_config_cmd.ConfigTestCase) ... ok
test_search_cpp (distutils.tests.test_config_cmd.ConfigTestCase) ... ok
test_run_setup_provides_file (distutils.tests.test_core.CoreTestCase) ... ok
test_run_setup_uses_current_dir (distutils.tests.test_core.CoreTestCase) ... ok
test_copy_tree_verbosity (distutils.tests.test_dir_util.DirUtilTestCase) ... ok
test_create_tree_verbosity (distutils.tests.test_dir_util.DirUtilTestCase) ... ok
test_mkpath_remove_tree_verbosity (distutils.tests.test_dir_util.DirUtilTestCase) ... ok
test_command_packages_cmdline (distutils.tests.test_dist.DistributionTestCase) ... ok
test_command_packages_configfile (distutils.tests.test_dist.DistributionTestCase) ... ok
test_command_packages_unspecified (distutils.tests.test_dist.DistributionTestCase) ... ok
test_empty_options (distutils.tests.test_dist.DistributionTestCase) ... ok
test_custom_pydistutils (distutils.tests.test_dist.MetadataTestCase) ... ok
test_obsoletes (distutils.tests.test_dist.MetadataTestCase) ... ok
test_obsoletes_illegal (distutils.tests.test_dist.MetadataTestCase) ... ok
test_provides (distutils.tests.test_dist.MetadataTestCase) ... ok
test_provides_illegal (distutils.tests.test_dist.MetadataTestCase) ... ok
test_requires (distutils.tests.test_dist.MetadataTestCase) ... ok
test_requires_illegal (distutils.tests.test_dist.MetadataTestCase) ... ok
test_simple_metadata (distutils.tests.test_dist.MetadataTestCase) ... ok
test_move_file_verbosity (distutils.tests.test_file_util.FileUtilTestCase) ... ok
test_glob_to_re (distutils.tests.test_filelist.FileListTestCase) ... ok
test_home_installation_scheme (distutils.tests.test_install.InstallTestCase) ... ok
test_user_site (distutils.tests.test_install.InstallTestCase) ... ok
test_simple_run (distutils.tests.test_install_data.InstallDataTestCase) ... ok
test_simple_run (distutils.tests.test_install_headers.InstallHeadersTestCase) ... ok
test_default_settings (distutils.tests.test_install_scripts.InstallScriptsTestCase) ... ok
test_installation (distutils.tests.test_install_scripts.InstallScriptsTestCase) ... ok
test_no_compiler (distutils.tests.test_msvc9compiler.msvc9compilerTestCase) ... ok
test_reg_class (distutils.tests.test_msvc9compiler.msvc9compilerTestCase) ... ok
test_create_pypirc (distutils.tests.test_register.registerTestCase) ... ok
test_password_not_in_file (distutils.tests.test_register.registerTestCase) ... ok
test_password_reset (distutils.tests.test_register.registerTestCase) ... ok
test_registering (distutils.tests.test_register.registerTestCase) ... ok
test_server_empty_registration (distutils.tests.test_register.registerTestCase) ... ok
test_server_registration (distutils.tests.test_register.registerTestCase) ... ok
test_add_defaults (distutils.tests.test_sdist.sdistTestCase) ... ok
test_make_distribution (distutils.tests.test_sdist.sdistTestCase) ... ok
test_prune_file_list (distutils.tests.test_sdist.sdistTestCase) ... ok
test_server_empty_registration (distutils.tests.test_sdist.sdistTestCase) ... ok
test_server_registration (distutils.tests.test_sdist.sdistTestCase) ... ok
test_nt_quote_args (distutils.tests.test_spawn.SpawnTestCase) ... ok
test_customize_compiler (distutils.tests.test_sysconfig.SysconfigTestCase) ... ok
test_get_config_h_filename (distutils.tests.test_sysconfig.SysconfigTestCase) ... ok
test_get_config_vars (distutils.tests.test_sysconfig.SysconfigTestCase) ... ok
test_get_python_inc (distutils.tests.test_sysconfig.SysconfigTestCase) ... ok
test_get_python_lib (distutils.tests.test_sysconfig.SysconfigTestCase) ... ok
test_class (distutils.tests.test_text_file.TextFileTestCase) ... ok
test_finalize_options (distutils.tests.test_upload.uploadTestCase) ... ok
test_saved_password (distutils.tests.test_upload.uploadTestCase) ... ok
test_server_empty_registration (distutils.tests.test_upload.uploadTestCase) ... ok
test_server_registration (distutils.tests.test_upload.uploadTestCase) ... ok
test_upload (distutils.tests.test_upload.uploadTestCase) ... ok
test_change_root (distutils.tests.test_util.utilTestCase) ... ok
test_check_environ (distutils.tests.test_util.utilTestCase) ... ok
test_convert_path (distutils.tests.test_util.utilTestCase) ... ok
test_get_platform (distutils.tests.test_util.utilTestCase) ... ok
test_rfc822_escape (distutils.tests.test_util.utilTestCase) ... ok
test_split_quoted (distutils.tests.test_util.utilTestCase) ... ok
test_strtobool (distutils.tests.test_util.utilTestCase) ... ok
test_cmp (distutils.tests.test_version.VersionTestCase) ... ok
test_cmp_strict (distutils.tests.test_version.VersionTestCase) ... ok
test_prerelease (distutils.tests.test_version.VersionTestCase) ... ok
Doctest: distutils.versionpredicate.VersionPredicate ... ok
Doctest: distutils.versionpredicate.split_provision ... ok

----------------------------------------------------------------------
Ran 97 tests in 2.646s

OK


My apologies for creating this much trouble.