I have the same issue. To be honest it is because I'm using MSVC2010. I know it is not a supported platform but the patch to fix the problem is really just the following (and it is compatible with MSVC2008):

--- Lib/distutils/msvc9compiler.py.orig Mon Jun 21 17:27:46 2010
+++ Lib/distutils/msvc9compiler.py      Mon Mar 12 13:23:56 2012
@@ -645,6 +645,7 @@
                     build_temp,
                     os.path.basename(output_filename) + ".manifest")
             ld_args.append('/MANIFESTFILE:' + temp_manifest)
+            ld_args.append('/MANIFEST')

             if extra_preargs:
                 ld_args[:0] = extra_preargs


On a side-note I wrote a CMakeLists.txt for python for windows. I have to say it was pretty easy even if I'm not building everything (I left out tcl/tk and bsddb). I would hope python in the future could use a more flexible way if being built. For reference, I copy here the cmakelists.txt.