I didn't say that the problems are because of the registry. I just hate the registry because it's a really bad, unusable way to configure the systems and turns into a mess and tightly binds everything together when it should all be loosely coupled. The INI file was a much better solution for configuring things.
Actually INI files are usually in a predictable place. It is registry entries that are spread all over the registry and are not cleaned-up when an application is uninstalled.