Does the problem still exist? Can you install and deinstall the package and install again and the configuration files are handled correctly?
It is possible the problem with the configurations was due to a broken INSTALL/DEINSTALL script that was included with the previously installed version. It has been proposed for future package installation tools to handle the configuration file processing. This means that improvements can be made to the tool instead of thousands of previously-created packages. (The way it is now means that any time a there is some bug or an improvement for this, then all packages that hve configurations would have to be rebuilt.)
