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Ok, this issue is worse, and much easier to reproduce, than I thought. Here is an updated ctypes_test.zip with a repro using only integers and callbacks.
Correct output:
('three', (1, 2, 3))
('four', (1, 2, 3, 4))
('five', (1, 2, 3, 4, 5))
Incorrect output:
('three', (1, 2, 3))
('four', (1, 2, 3, 0))
('five', (1, 2, 3, 0, 5))
I built Python 2.7 from source with MSVC 9. This is not reproducible in Debug mode, or Win32 Release mode. It only happens in x64 Release mode. 
One very interesting discovery is that if I set these options:
Optimization: Disabled (/Od)
Enable Instrinsic Functions: No
the error does not occur!