When I submit my package to the Python Package Index (https://pypi.python.org/pypi) my README file, which is written with valid reStructuredText and saved as README.rst, is displayed as plain text without any formatting.
I have run it through validators (rstctl and collective.checkdocs) and no errors are returned.
My package is at: https://pypi.python.org/pypi/lcinvestor
It's in github at: https://github.com/jgillick/LendingClubAutoInvestor
It turns out that the answer from @sigmavirus regarding the links was close. I started a discussion on the distutils mailing list and found out that in-page links (i.e. #minimum-cash) are not allowed by the pypi reStructuredText parser and will invalidate the entire document.
It seems that pypi uses a whitelist to filter link protocols (http vs ftp vs gopher), and sees '#' as an invalid protocol. It seems like this would be pretty easy to fix on their end, but until then, I'll be removing my in-page anchor links.