The attachment of my sample email contains '123\n', but get_payload
(decode=True) returns '123'.
The source of this error is the function _bdecode from the email.utils 
module, which gets called for decoding base64 encoded payloads. Here 
the last \n gets stripped away, because (comment in the function):

# We can't quite use base64.encodestring() since it tacks on a "courtesy
# newline".  Blech!

I don't think that's true. At least not for Python 2.5.4 and upwards. 
Also note the "encodestring" instead of "decodestring".
In fact calling

base64.decodestring(part.get_payload())

returns the correct value, so I propose to remove this function 
completely and just use the standard decoding method.
Please note that base64.encodestring really tacks on a \n.