Over in Ubuntu, we inherit Debian's python-configparser package, which currently provides configparser 3.3.0r2. Normally, this package isn't hugely depended on by other packages, so it doesn't get installed very often. Recently one of our main packages created a dependency on configparser and when it got installed lots of things broke. We ended up having to rewrite the code to not depend on configparser, and thus relegating it back away from our main repository. We must actively recommend against installing it.
Here are examples of things it broke. Some have been fixed in the broken package, but a few (e.g. the virtualenv problem) is currently fixable only by de-installing configparser.
Unfortunately, I don't have a lot of time right now for further investigation, but I wanted to file the bug upstream for tracking purposes.