This post is mostly for my own reference for the future.
I ran into trouble when using clang with 64 bit ctypes on a windows machine. Apparently there's a bug reported on the issue.
On windows, the compiler will convert arguments larger than 8 bytes into references automatically, whereas ctypes just happily allocates memory for the stack, ignoring the this fact. That leads to crashes.
I tried recompiling the _ctypes.pyd file, but that only caused my Python to hang. So, until that bug is fixed, I have to use the POINTER construct in ctypes instead.
The guys implementing the Sublime autocompletion plugin has solved it this way: cindex.py