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The trigger of that exception is importlib._bootstrap._sanity_check() (http://hg.python.org/cpython/file/5e025dc7d728/Lib/importlib/_bootstrap.py#l1466). It's called very early on to verify certain things, including that the parent package is already loaded when importing a submodule. It's that last bit that's failing.
If you look at 3.2 vs. 3.3 for imp.load_dynamic() which does extension module loading for importlib, there is essentially no change, even as far as looking into Python/importdl.c:_PyImport_LoadDynamicModule() (http://hg.python.org/cpython/file/5e025dc7d728/Python/import.c#l1773 vs. http://hg.python.org/cpython/file/3654c711019a/Python/import.c#l3446).
The problem is that the check for the parent module is also in Python/import.c from 3.2 so this isn't a new check. Is it possible that Cython is doing something differently now that it didn't do before? I know you said this worked in 3.2 and earlier, Stefan, but was that with the same version of Cython? Did the actual C call and setup for that call change? Otherwise I can't think of how anything specifically changed between 3.2 and 3.3 that would fundamentally change this.