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The argument-passing code for passing structs larger than 8 bytes is broken on 64-bit Windows, leading to potential segmentation faults or other unpredictable behaviour. According to 
 http://msdn.microsoft.com/en-us/library/zthk2dkh.aspx
structs not of size 1, 2, 4 or 8 bytes should be passed by pointer. ctypes instead puts sizeof(struct) bytes onto the stack. The offending code is in ffi_prep_args in /Modules/_ctypes/libffi_msvc/ffi.c, which apparently hasn't been kept up to date with the /Modules/_ctypes/libffi/src/x86/ffi.c. The latter module works correctly: it has an extra #ifdef X86_WIN64 block (shown below) to take care of structs not of size 1, 2, 4 or 8. That block is missing in the libffi_msvc version.
 z = (*p_arg)->size;
#ifdef X86_WIN64
 if (z > sizeof(ffi_arg)
 || ((*p_arg)->type == FFI_TYPE_STRUCT
 && (z != 1 && z != 2 && z != 4 && z != 8))
#if FFI_TYPE_DOUBLE != FFI_TYPE_LONGDOUBLE
 || ((*p_arg)->type == FFI_TYPE_LONGDOUBLE)
#endif
 )
 {
 z = sizeof(ffi_arg);
 *(void **)argp = *p_argv;
 }
 else if ((*p_arg)->type == FFI_TYPE_FLOAT)
 {
 memcpy(argp, *p_argv, z);
 }
 else
#endif
It looks to me as though issue 17310 may be related.
Credit for this discovery should go to Freek Mank.