> When a file is opened in append mode, the operating system guarantees
> that all write(2) system calls atomically appended their payload to the 
> file.

Does it? I don't see such strong guarantees in http://pubs.opengroup.org/onlinepubs/9699919799/functions/write.html

In any case, Python 2 uses fwrite() not write(), so it may be the explanation. Do you observe the same behaviour when using io.open() instead of open()?

(io.open() is the Python 3 IO stack backported to Python 2)