Thomas Levine added the comment:

Hmm now it looks to me like this is the intended behavior.
http://hg.python.org/cpython/file/ea0aa3e32ab5/Lib/test/test_configparser.py#l1541

Switching the single percent sign (%) to two (%%) in .pypirc makes it work. 
Maybe we can make a nicer error message though.

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