The 0.98.5 windows installer is still overwriting existing installations of configobj. This package is not needed by matplotlib and should not be installed on windows, nor should traits.
I have removed configobj and enthought.traits from the trunk, but it is still present on the maintenance branches. On build systems, setup.cfg for the maintenance branches should be configured to not install configobj or traits under any circumstances. Once it has been so configured, the build directory needs to be deleted, because it probably contains a cached copy of configobj that will get incorporated into the installer the next time it is built, regardless of the settings in setup.cfg.
This bug has been assigned to me, but it is out of my hands at this point.