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I've not tested this on Windows. It was developed on Debian. The error you show does not look to me to be related to platform differences. It's been a while that I've used this code so maybe this multiple of 16 is a new requirement in the Crypto module(?).
Is it possible to zero-pad the ciphertext payload out to a multiple of 16 before the decrypt and recover the plaintext?
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Better late than never: I found the problem on Windows being that read() stops at EOF when the file is not explicitly opened in binary mode. See also http://stackoverflow.com/questions/9905874/python-does-not-read-entire-text-file
The payload of a database file must always be a multple of 16 bytes.
Opening the database with fp = open(filename, "rb")
(kpdb.py:Database:read) solves the problem.
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