Are you making a debug build? It might be looking for _ctypes_d.pyd in that case. You'll need a release build for the embeddable distro, as well as including the pyds from the zip in sys.path - they need to be standalone files.

The embeddable release is meant only for redistribution, so you should build and test against a full install (including debug binaries if you want) and do integration testing with the embeddable package and a release build. (So Zach, yes, it's deliberate.)